6JLJ

XFEL structure of cyanobacterial photosystem II (dark state, dataset1)

PDB DOI: https://doi.org/10.2210/pdb6JLJ/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Thermostichus vulcanus
Mutation(s): No
Membrane Protein: Yes PDBTMmpstruc

Deposited: 2019-03-06 Released: 2019-10-16
Deposition Author(s): Suga, M., Shen, J.R.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 ?
R-Value Free: 0.198
R-Value Work: 0.152
R-Value Observed: 0.154

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser.

Suga, M., Akita, F., Yamashita, K., Nakajima, Y., Ueno, G., Li, H., Yamane, T., Hirata, K., Umena, Y., Yonekura, S., Yu, L.J., Murakami, H., Nomura, T., Kimura, T., Kubo, M., Baba, S., Kumasaka, T., Tono, K., Yabashi, M., Isobe, H., Yamaguchi, K., Yamamoto, M., Ago, H., Shen, J.R.

(2019) Science 366: 334-338

PubMed: 31624207 Search on PubMed
DOI: https://doi.org/10.1126/science.aax6998
Primary Citation of Related Structures:
6JLJ, 6JLK, 6JLL, 6JLM, 6JLN, 6JLO, 6JLP

PubMed Abstract:
Photosynthetic water oxidation is catalyzed by the Mn ₄CaO ₅ cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S ₀ to S ₄). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S ₁, S ₂, and S ₃ states by x-ray free-electron laser serial crystallography. No insertion of water was found in S ₂, but flipping of D1 Glu ¹⁸⁹ upon transition to S ₃ leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn ₄CaO ₆ cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

Organizational Affiliation

Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan. michisuga@okayama-u.ac.jp ago@spring8.or.jp shen@cc.okayama-u.ac.jp.

Macromolecule Content

Total Structure Weight: 729.59 kDa
Atom Count: 54,101
Modelled Residue Count: 5,293
Deposited Residue Count: 5,384
Unique protein chains: 20

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	A, U [auth a]	344	Thermostichus vulcanus	Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P51765 (Thermostichus vulcanus) Explore P51765 Go to UniProtKB: P51765
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UniProt Group	P51765
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	B, V [auth b]	505	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus) Explore D0VWR1 Go to UniProtKB: D0VWR1
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UniProt Group	D0VWR1
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	C, W [auth c]	455	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR7 (Thermostichus vulcanus) Explore D0VWR7 Go to UniProtKB: D0VWR7
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UniProt Group	D0VWR7
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D, X [auth d]	342	Thermostichus vulcanus	Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus) Explore D0VWR8 Go to UniProtKB: D0VWR8
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UniProt Group	D0VWR8
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E, Y [auth e]	84	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12238 (Thermostichus vulcanus) Explore P12238 Go to UniProtKB: P12238
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UniProt Group	P12238
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F, Z [auth f]	44	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12239 (Thermostichus vulcanus) Explore P12239 Go to UniProtKB: P12239
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UniProt Group	P12239
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	AA [auth h], G [auth H]	65	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P19052 (Thermostichus vulcanus) Explore P19052 Go to UniProtKB: P19052
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UniProt Group	P19052
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	BA [auth i], H [auth I]	38	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12240 (Thermostichus vulcanus) Explore P12240 Go to UniProtKB: P12240
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UniProt Group	P12240
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	CA [auth j], I [auth J]	39	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus) Explore Q7DGD4 Go to UniProtKB: Q7DGD4
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UniProt Group	Q7DGD4
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	DA [auth k], J [auth K]	37	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P19054 (Thermostichus vulcanus) Explore P19054 Go to UniProtKB: P19054
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UniProt Group	P19054
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	EA [auth l], K [auth L]	37	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12241 (Thermostichus vulcanus) Explore P12241 Go to UniProtKB: P12241
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UniProt Group	P12241
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	FA [auth m], L [auth M]	36	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12312 (Thermostichus vulcanus) Explore P12312 Go to UniProtKB: P12312
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UniProt Group	P12312
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II manganese-stabilizing polypeptide	GA [auth o], M [auth O]	244	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR2 (Thermostichus vulcanus) Explore D0VWR2 Go to UniProtKB: D0VWR2
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UniProt Group	D0VWR2
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	HA [auth t], N [auth T]	32	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for P12313 (Thermostichus vulcanus) Explore P12313 Go to UniProtKB: P12313
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UniProt Group	P12313
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 12 kDa extrinsic protein	IA [auth u], O [auth U]	104	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P56152 (Thermostichus vulcanus) Explore P56152 Go to UniProtKB: P56152
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UniProt Group	P56152
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	JA [auth v], P [auth V]	137	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A387 (Thermostichus vulcanus) Explore P0A387 Go to UniProtKB: P0A387
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UniProt Group	P0A387
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Ycf12	KA [auth y], Q [auth Y]	30	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus) Explore D0VWR3 Go to UniProtKB: D0VWR3
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UniProt Group	D0VWR3
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein X	LA [auth x], R [auth X]	40	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus) Explore D0VWR4 Go to UniProtKB: D0VWR4
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UniProt Group	D0VWR4
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	MA [auth z], S [auth Z]	62	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus) Explore D0VWR5 Go to UniProtKB: D0VWR5
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UniProt Group	D0VWR5
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein Y	T [auth R]	34	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus) Explore P0DM37 Go to UniProtKB: P0DM37
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UniProt Group	P0DM37
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Reference Sequence

Small Molecules

Ligands 19 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD Query on DGD Download Ideal Coordinates CCD File SDF format, chain CJ [auth e] SDF format, chain GD [auth C] SDF format, chain GI [auth c] SDF format, chain HD [auth C] SDF format, chain HI [auth c] SDF format, chain ID [auth C] SDF format, chain II [auth c] SDF format, chain KJ [auth h] SDF format, chain LE [auth H] SDF format, chain XD [auth D] MOL2 format, chain CJ [auth e] MOL2 format, chain GD [auth C] MOL2 format, chain GI [auth c] MOL2 format, chain HD [auth C] MOL2 format, chain HI [auth c] MOL2 format, chain ID [auth C] MOL2 format, chain II [auth c] MOL2 format, chain KJ [auth h] MOL2 format, chain LE [auth H] MOL2 format, chain XD [auth D] mmCIF format, chain CJ [auth e] mmCIF format, chain GD [auth C] mmCIF format, chain GI [auth c] mmCIF format, chain HD [auth C] mmCIF format, chain HI [auth c] mmCIF format, chain ID [auth C] mmCIF format, chain II [auth c] mmCIF format, chain KJ [auth h] mmCIF format, chain LE [auth H] mmCIF format, chain XD [auth D]	CJ [auth e] GD [auth C] GI [auth c] HD [auth C] HI [auth c] CJ [auth e], GD [auth C], GI [auth c], HD [auth C], HI [auth c], ID [auth C], II [auth c], KJ [auth h], LE [auth H], XD [auth D]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain CJ [auth e] Focus chain GD [auth C] Focus chain GI [auth c] Focus chain HD [auth C] Focus chain HI [auth c] Focus chain ID [auth C] Focus chain II [auth c] Focus chain KJ [auth h] Focus chain LE [auth H] Focus chain XD [auth D] Interactions & Density Focus chain CJ [auth e] Focus chain GD [auth C] Focus chain GI [auth c] Focus chain HD [auth C] Focus chain HI [auth c] Focus chain ID [auth C] Focus chain II [auth c] Focus chain KJ [auth h] Focus chain LE [auth H] Focus chain XD [auth D]
CLA Query on CLA Download Ideal Coordinates CCD File SDF format, chain AD [auth C] SDF format, chain AH [auth b] SDF format, chain AI [auth c] SDF format, chain BD [auth C] SDF format, chain BH [auth b] SDF format, chain BI [auth c] SDF format, chain CD [auth C] SDF format, chain CH [auth b] SDF format, chain CI [auth c] SDF format, chain DD [auth C] SDF format, chain DH [auth b] SDF format, chain DI [auth c] SDF format, chain EH [auth b] SDF format, chain EI [auth c] SDF format, chain FH [auth b] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain NB [auth B] SDF format, chain OB [auth B] SDF format, chain PB [auth B] SDF format, chain QB [auth B] SDF format, chain QG [auth b] SDF format, chain QI [auth d] SDF format, chain RA [auth A] SDF format, chain RB [auth B] SDF format, chain RC [auth C] SDF format, chain RG [auth b] SDF format, chain RI [auth d] SDF format, chain SA [auth A] SDF format, chain SB [auth B] SDF format, chain SC [auth C] SDF format, chain SG [auth b] SDF format, chain SH [auth c] SDF format, chain SI [auth d] SDF format, chain TA [auth A] SDF format, chain TB [auth B] SDF format, chain TC [auth C] SDF format, chain TD [auth D] SDF format, chain TG [auth b] SDF format, chain TH [auth c] SDF format, chain UB [auth B] SDF format, chain UC [auth C] SDF format, chain UD [auth D] SDF format, chain UG [auth b] SDF format, chain UH [auth c] SDF format, chain VA [auth A] SDF format, chain VB [auth B] SDF format, chain VC [auth C] SDF format, chain VG [auth b] SDF format, chain VH [auth c] SDF format, chain WB [auth B] SDF format, chain WC [auth C] SDF format, chain WF [auth a] SDF format, chain WG [auth b] SDF format, chain WH [auth c] SDF format, chain XC [auth C] SDF format, chain XF [auth a] SDF format, chain XG [auth b] SDF format, chain XH [auth c] SDF format, chain YC [auth C] SDF format, chain YG [auth b] SDF format, chain YH [auth c] SDF format, chain ZC [auth C] SDF format, chain ZF [auth a] SDF format, chain ZG [auth b] SDF format, chain ZH [auth c] MOL2 format, chain AD [auth C] MOL2 format, chain AH [auth b] MOL2 format, chain AI [auth c] MOL2 format, chain BD [auth C] MOL2 format, chain BH [auth b] MOL2 format, chain BI [auth c] MOL2 format, chain CD [auth C] MOL2 format, chain CH [auth b] MOL2 format, chain CI [auth c] MOL2 format, chain DD [auth C] MOL2 format, chain DH [auth b] MOL2 format, chain DI [auth c] MOL2 format, chain EH [auth b] MOL2 format, chain EI [auth c] MOL2 format, chain FH [auth b] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain NB [auth B] MOL2 format, chain OB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain QB [auth B] MOL2 format, chain QG [auth b] MOL2 format, chain QI [auth d] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain RC [auth C] MOL2 format, chain RG [auth b] MOL2 format, chain RI [auth d] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain SC [auth C] MOL2 format, chain SG [auth b] MOL2 format, chain SH [auth c] MOL2 format, chain SI [auth d] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth B] MOL2 format, chain TC [auth C] MOL2 format, chain TD [auth D] MOL2 format, chain TG [auth b] MOL2 format, chain TH [auth c] MOL2 format, chain UB [auth B] MOL2 format, chain UC [auth C] MOL2 format, chain UD [auth D] MOL2 format, chain UG [auth b] MOL2 format, chain UH [auth c] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain VC [auth C] MOL2 format, chain VG [auth b] MOL2 format, chain VH [auth c] MOL2 format, chain WB [auth B] MOL2 format, chain WC [auth C] MOL2 format, chain WF [auth a] MOL2 format, chain WG [auth b] MOL2 format, chain WH [auth c] MOL2 format, chain XC [auth C] MOL2 format, chain XF [auth a] MOL2 format, chain XG [auth b] MOL2 format, chain XH [auth c] MOL2 format, chain YC [auth C] MOL2 format, chain YG [auth b] MOL2 format, chain YH [auth c] MOL2 format, chain ZC [auth C] MOL2 format, chain ZF [auth a] MOL2 format, chain ZG [auth b] MOL2 format, chain ZH [auth c] mmCIF format, chain AD [auth C] mmCIF format, chain AH [auth b] mmCIF format, chain AI [auth c] mmCIF format, chain BD [auth C] mmCIF format, chain BH [auth b] mmCIF format, chain BI [auth c] mmCIF format, chain CD [auth C] mmCIF format, chain CH [auth b] mmCIF format, chain CI [auth c] mmCIF format, chain DD [auth C] mmCIF format, chain DH [auth b] mmCIF format, chain DI [auth c] mmCIF format, chain EH [auth b] mmCIF format, chain EI [auth c] mmCIF format, chain FH [auth b] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain NB [auth B] mmCIF format, chain OB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain QB [auth B] mmCIF format, chain QG [auth b] mmCIF format, chain QI [auth d] mmCIF format, chain RA [auth A] mmCIF format, chain RB [auth B] mmCIF format, chain RC [auth C] mmCIF format, chain RG [auth b] mmCIF format, chain RI [auth d] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth B] mmCIF format, chain SC [auth C] mmCIF format, chain SG [auth b] mmCIF format, chain SH [auth c] mmCIF format, chain SI [auth d] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth B] mmCIF format, chain TC [auth C] mmCIF format, chain TD [auth D] mmCIF format, chain TG [auth b] mmCIF format, chain TH [auth c] mmCIF format, chain UB [auth B] mmCIF format, chain UC [auth C] mmCIF format, chain UD [auth D] mmCIF format, chain UG [auth b] mmCIF format, chain UH [auth c] mmCIF format, chain VA [auth A] mmCIF format, chain VB [auth B] mmCIF format, chain VC [auth C] mmCIF format, chain VG [auth b] mmCIF format, chain VH [auth c] mmCIF format, chain WB [auth B] mmCIF format, chain WC [auth C] mmCIF format, chain WF [auth a] mmCIF format, chain WG [auth b] mmCIF format, chain WH [auth c] mmCIF format, chain XC [auth C] mmCIF format, chain XF [auth a] mmCIF format, chain XG [auth b] mmCIF format, chain XH [auth c] mmCIF format, chain YC [auth C] mmCIF format, chain YG [auth b] mmCIF format, chain YH [auth c] mmCIF format, chain ZC [auth C] mmCIF format, chain ZF [auth a] mmCIF format, chain ZG [auth b] mmCIF format, chain ZH [auth c]	AD [auth C] AH [auth b] AI [auth c] BD [auth C] BH [auth b] AD [auth C], AH [auth b], AI [auth c], BD [auth C], BH [auth b], BI [auth c], CD [auth C], CH [auth b], CI [auth c], DD [auth C], DH [auth b], DI [auth c], EH [auth b], EI [auth c], FH [auth b], HB [auth B], IB [auth B], JB [auth B], KB [auth B], LB [auth B], MB [auth B], NB [auth B], OB [auth B], PB [auth B], QB [auth B], QG [auth b], QI [auth d], RA [auth A], RB [auth B], RC [auth C], RG [auth b], RI [auth d], SA [auth A], SB [auth B], SC [auth C], SG [auth b], SH [auth c], SI [auth d], TA [auth A], TB [auth B], TC [auth C], TD [auth D], TG [auth b], TH [auth c], UB [auth B], UC [auth C], UD [auth D], UG [auth b], UH [auth c], VA [auth A], VB [auth B], VC [auth C], VG [auth b], VH [auth c], WB [auth B], WC [auth C], WF [auth a], WG [auth b], WH [auth c], XC [auth C], XF [auth a], XG [auth b], XH [auth c], YC [auth C], YG [auth b], YH [auth c], ZC [auth C], ZF [auth a], ZG [auth b], ZH [auth c]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AD [auth C] Focus chain AH [auth b] Focus chain AI [auth c] Focus chain BD [auth C] Focus chain BH [auth b] Focus chain BI [auth c] Focus chain CD [auth C] Focus chain CH [auth b] Focus chain CI [auth c] Focus chain DD [auth C] Focus chain DH [auth b] Focus chain DI [auth c] Focus chain EH [auth b] Focus chain EI [auth c] Focus chain FH [auth b] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain QG [auth b] Focus chain QI [auth d] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain RC [auth C] Focus chain RG [auth b] Focus chain RI [auth d] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain SC [auth C] Focus chain SG [auth b] Focus chain SH [auth c] Focus chain SI [auth d] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain TC [auth C] Focus chain TD [auth D] Focus chain TG [auth b] Focus chain TH [auth c] Focus chain UB [auth B] Focus chain UC [auth C] Focus chain UD [auth D] Focus chain UG [auth b] Focus chain UH [auth c] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain VC [auth C] Focus chain VG [auth b] Focus chain VH [auth c] Focus chain WB [auth B] Focus chain WC [auth C] Focus chain WF [auth a] Focus chain WG [auth b] Focus chain WH [auth c] Focus chain XC [auth C] Focus chain XF [auth a] Focus chain XG [auth b] Focus chain XH [auth c] Focus chain YC [auth C] Focus chain YG [auth b] Focus chain YH [auth c] Focus chain ZC [auth C] Focus chain ZF [auth a] Focus chain ZG [auth b] Focus chain ZH [auth c] Interactions & Density Focus chain AD [auth C] Focus chain AH [auth b] Focus chain AI [auth c] Focus chain BD [auth C] Focus chain BH [auth b] Focus chain BI [auth c] Focus chain CD [auth C] Focus chain CH [auth b] Focus chain CI [auth c] Focus chain DD [auth C] Focus chain DH [auth b] Focus chain DI [auth c] Focus chain EH [auth b] Focus chain EI [auth c] Focus chain FH [auth b] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain QG [auth b] Focus chain QI [auth d] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain RC [auth C] Focus chain RG [auth b] Focus chain RI [auth d] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain SC [auth C] Focus chain SG [auth b] Focus chain SH [auth c] Focus chain SI [auth d] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain TC [auth C] Focus chain TD [auth D] Focus chain TG [auth b] Focus chain TH [auth c] Focus chain UB [auth B] Focus chain UC [auth C] Focus chain UD [auth D] Focus chain UG [auth b] Focus chain UH [auth c] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain VC [auth C] Focus chain VG [auth b] Focus chain VH [auth c] Focus chain WB [auth B] Focus chain WC [auth C] Focus chain WF [auth a] Focus chain WG [auth b] Focus chain WH [auth c] Focus chain XC [auth C] Focus chain XF [auth a] Focus chain XG [auth b] Focus chain XH [auth c] Focus chain YC [auth C] Focus chain YG [auth b] Focus chain YH [auth c] Focus chain ZC [auth C] Focus chain ZF [auth a] Focus chain ZG [auth b] Focus chain ZH [auth c]
PHO Query on PHO Download Ideal Coordinates CCD File SDF format, chain PI [auth d] SDF format, chain SD [auth D] SDF format, chain UA [auth A] SDF format, chain YF [auth a] MOL2 format, chain PI [auth d] MOL2 format, chain SD [auth D] MOL2 format, chain UA [auth A] MOL2 format, chain YF [auth a] mmCIF format, chain PI [auth d] mmCIF format, chain SD [auth D] mmCIF format, chain UA [auth A] mmCIF format, chain YF [auth a]	PI [auth d], SD [auth D], UA [auth A], YF [auth a]	PHEOPHYTIN A C₅₅ H₇₄ N₄ O₅ CQIKWXUXPNUNDV-RCBXBCQGSA-N		Interactions Focus chain PI [auth d] Focus chain SD [auth D] Focus chain UA [auth A] Focus chain YF [auth a] Interactions & Density Focus chain PI [auth d] Focus chain SD [auth D] Focus chain UA [auth A] Focus chain YF [auth a]
SQD Query on SQD Download Ideal Coordinates CCD File SDF format, chain AC [auth B] SDF format, chain BB [auth A] SDF format, chain BG [auth a] SDF format, chain GJ [auth f] SDF format, chain IE [auth F] SDF format, chain SE [auth L] SDF format, chain SF [auth a] SDF format, chain XA [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain BB [auth A] MOL2 format, chain BG [auth a] MOL2 format, chain GJ [auth f] MOL2 format, chain IE [auth F] MOL2 format, chain SE [auth L] MOL2 format, chain SF [auth a] MOL2 format, chain XA [auth A] mmCIF format, chain AC [auth B] mmCIF format, chain BB [auth A] mmCIF format, chain BG [auth a] mmCIF format, chain GJ [auth f] mmCIF format, chain IE [auth F] mmCIF format, chain SE [auth L] mmCIF format, chain SF [auth a] mmCIF format, chain XA [auth A]	AC [auth B] BB [auth A] BG [auth a] GJ [auth f] IE [auth F] AC [auth B], BB [auth A], BG [auth a], GJ [auth f], IE [auth F], SE [auth L], SF [auth a], XA [auth A]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C₄₁ H₇₈ O₁₂ S RVUUQPKXGDTQPG-JUDHQOGESA-N		Interactions Focus chain AC [auth B] Focus chain BB [auth A] Focus chain BG [auth a] Focus chain GJ [auth f] Focus chain IE [auth F] Focus chain SE [auth L] Focus chain SF [auth a] Focus chain XA [auth A] Interactions & Density Focus chain AC [auth B] Focus chain BB [auth A] Focus chain BG [auth a] Focus chain GJ [auth f] Focus chain IE [auth F] Focus chain SE [auth L] Focus chain SF [auth a] Focus chain XA [auth A]
LMG Query on LMG Download Ideal Coordinates CCD File SDF format, chain CG [auth a] SDF format, chain DK [auth z] SDF format, chain JD [auth C] SDF format, chain JH [auth b] SDF format, chain JI [auth c] SDF format, chain KD [auth C] SDF format, chain KI [auth c] SDF format, chain MJ [auth j] SDF format, chain NE [auth J] SDF format, chain NF [auth Z] SDF format, chain QC [auth C] SDF format, chain TE [auth M] MOL2 format, chain CG [auth a] MOL2 format, chain DK [auth z] MOL2 format, chain JD [auth C] MOL2 format, chain JH [auth b] MOL2 format, chain JI [auth c] MOL2 format, chain KD [auth C] MOL2 format, chain KI [auth c] MOL2 format, chain MJ [auth j] MOL2 format, chain NE [auth J] MOL2 format, chain NF [auth Z] MOL2 format, chain QC [auth C] MOL2 format, chain TE [auth M] mmCIF format, chain CG [auth a] mmCIF format, chain DK [auth z] mmCIF format, chain JD [auth C] mmCIF format, chain JH [auth b] mmCIF format, chain JI [auth c] mmCIF format, chain KD [auth C] mmCIF format, chain KI [auth c] mmCIF format, chain MJ [auth j] mmCIF format, chain NE [auth J] mmCIF format, chain NF [auth Z] mmCIF format, chain QC [auth C] mmCIF format, chain TE [auth M]	CG [auth a] DK [auth z] JD [auth C] JH [auth b] JI [auth c] CG [auth a], DK [auth z], JD [auth C], JH [auth b], JI [auth c], KD [auth C], KI [auth c], MJ [auth j], NE [auth J], NF [auth Z], QC [auth C], TE [auth M]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain CG [auth a] Focus chain DK [auth z] Focus chain JD [auth C] Focus chain JH [auth b] Focus chain JI [auth c] Focus chain KD [auth C] Focus chain KI [auth c] Focus chain MJ [auth j] Focus chain NE [auth J] Focus chain NF [auth Z] Focus chain QC [auth C] Focus chain TE [auth M] Interactions & Density Focus chain CG [auth a] Focus chain DK [auth z] Focus chain JD [auth C] Focus chain JH [auth b] Focus chain JI [auth c] Focus chain KD [auth C] Focus chain KI [auth c] Focus chain MJ [auth j] Focus chain NE [auth J] Focus chain NF [auth Z] Focus chain QC [auth C] Focus chain TE [auth M]
PL9 Query on PL9 Download Ideal Coordinates CCD File SDF format, chain DG [auth a] SDF format, chain EB [auth A] SDF format, chain UI [auth d] SDF format, chain WD [auth D] MOL2 format, chain DG [auth a] MOL2 format, chain EB [auth A] MOL2 format, chain UI [auth d] MOL2 format, chain WD [auth D] mmCIF format, chain DG [auth a] mmCIF format, chain EB [auth A] mmCIF format, chain UI [auth d] mmCIF format, chain WD [auth D]	DG [auth a], EB [auth A], UI [auth d], WD [auth D]	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE C₅₃ H₈₀ O₂ FKUYMLZIRPABFK-UHFFFAOYSA-N		Interactions Focus chain DG [auth a] Focus chain EB [auth A] Focus chain UI [auth d] Focus chain WD [auth D] Interactions & Density Focus chain DG [auth a] Focus chain EB [auth A] Focus chain UI [auth d] Focus chain WD [auth D]
LHG Query on LHG Download Ideal Coordinates CCD File SDF format, chain AE [auth D] SDF format, chain DJ [auth e] SDF format, chain EE [auth E] SDF format, chain QJ [auth l] SDF format, chain RE [auth L] SDF format, chain VI [auth d] SDF format, chain WI [auth d] SDF format, chain XI [auth d] SDF format, chain YD [auth D] SDF format, chain ZD [auth D] MOL2 format, chain AE [auth D] MOL2 format, chain DJ [auth e] MOL2 format, chain EE [auth E] MOL2 format, chain QJ [auth l] MOL2 format, chain RE [auth L] MOL2 format, chain VI [auth d] MOL2 format, chain WI [auth d] MOL2 format, chain XI [auth d] MOL2 format, chain YD [auth D] MOL2 format, chain ZD [auth D] mmCIF format, chain AE [auth D] mmCIF format, chain DJ [auth e] mmCIF format, chain EE [auth E] mmCIF format, chain QJ [auth l] mmCIF format, chain RE [auth L] mmCIF format, chain VI [auth d] mmCIF format, chain WI [auth d] mmCIF format, chain XI [auth d] mmCIF format, chain YD [auth D] mmCIF format, chain ZD [auth D]	AE [auth D] DJ [auth e] EE [auth E] QJ [auth l] RE [auth L] AE [auth D], DJ [auth e], EE [auth E], QJ [auth l], RE [auth L], VI [auth d], WI [auth d], XI [auth d], YD [auth D], ZD [auth D]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain AE [auth D] Focus chain DJ [auth e] Focus chain EE [auth E] Focus chain QJ [auth l] Focus chain RE [auth L] Focus chain VI [auth d] Focus chain WI [auth d] Focus chain XI [auth d] Focus chain YD [auth D] Focus chain ZD [auth D] Interactions & Density Focus chain AE [auth D] Focus chain DJ [auth e] Focus chain EE [auth E] Focus chain QJ [auth l] Focus chain RE [auth L] Focus chain VI [auth d] Focus chain WI [auth d] Focus chain XI [auth d] Focus chain YD [auth D] Focus chain ZD [auth D]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain BK [auth v] SDF format, chain EJ [auth e] SDF format, chain FE [auth E] SDF format, chain JF [auth V] MOL2 format, chain BK [auth v] MOL2 format, chain EJ [auth e] MOL2 format, chain FE [auth E] MOL2 format, chain JF [auth V] mmCIF format, chain BK [auth v] mmCIF format, chain EJ [auth e] mmCIF format, chain FE [auth E] mmCIF format, chain JF [auth V]	BK [auth v], EJ [auth e], FE [auth E], JF [auth V]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BK [auth v] Focus chain EJ [auth e] Focus chain FE [auth E] Focus chain JF [auth V] Interactions & Density Focus chain BK [auth v] Focus chain EJ [auth e] Focus chain FE [auth E] Focus chain JF [auth V]
BCR Query on BCR Download Ideal Coordinates CCD File SDF format, chain AG [auth a] SDF format, chain CF [auth T] SDF format, chain CK [auth y] SDF format, chain ED [auth C] SDF format, chain FD [auth C] SDF format, chain FI [auth c] SDF format, chain GH [auth b] SDF format, chain HH [auth b] SDF format, chain IH [auth b] SDF format, chain JJ [auth h] SDF format, chain KE [auth H] SDF format, chain LF [auth Y] SDF format, chain OI [auth c] SDF format, chain PJ [auth k] SDF format, chain QE [auth K] SDF format, chain TI [auth d] SDF format, chain VD [auth D] SDF format, chain VJ [auth t] SDF format, chain WA [auth A] SDF format, chain XB [auth B] SDF format, chain YB [auth B] SDF format, chain ZB [auth B] MOL2 format, chain AG [auth a] MOL2 format, chain CF [auth T] MOL2 format, chain CK [auth y] MOL2 format, chain ED [auth C] MOL2 format, chain FD [auth C] MOL2 format, chain FI [auth c] MOL2 format, chain GH [auth b] MOL2 format, chain HH [auth b] MOL2 format, chain IH [auth b] MOL2 format, chain JJ [auth h] MOL2 format, chain KE [auth H] MOL2 format, chain LF [auth Y] MOL2 format, chain OI [auth c] MOL2 format, chain PJ [auth k] MOL2 format, chain QE [auth K] MOL2 format, chain TI [auth d] MOL2 format, chain VD [auth D] MOL2 format, chain VJ [auth t] MOL2 format, chain WA [auth A] MOL2 format, chain XB [auth B] MOL2 format, chain YB [auth B] MOL2 format, chain ZB [auth B] mmCIF format, chain AG [auth a] mmCIF format, chain CF [auth T] mmCIF format, chain CK [auth y] mmCIF format, chain ED [auth C] mmCIF format, chain FD [auth C] mmCIF format, chain FI [auth c] mmCIF format, chain GH [auth b] mmCIF format, chain HH [auth b] mmCIF format, chain IH [auth b] mmCIF format, chain JJ [auth h] mmCIF format, chain KE [auth H] mmCIF format, chain LF [auth Y] mmCIF format, chain OI [auth c] mmCIF format, chain PJ [auth k] mmCIF format, chain QE [auth K] mmCIF format, chain TI [auth d] mmCIF format, chain VD [auth D] mmCIF format, chain VJ [auth t] mmCIF format, chain WA [auth A] mmCIF format, chain XB [auth B] mmCIF format, chain YB [auth B] mmCIF format, chain ZB [auth B]	AG [auth a] CF [auth T] CK [auth y] ED [auth C] FD [auth C] AG [auth a], CF [auth T], CK [auth y], ED [auth C], FD [auth C], FI [auth c], GH [auth b], HH [auth b], IH [auth b], JJ [auth h], KE [auth H], LF [auth Y], OI [auth c], PJ [auth k], QE [auth K], TI [auth d], VD [auth D], VJ [auth t], WA [auth A], XB [auth B], YB [auth B], ZB [auth B]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain AG [auth a] Focus chain CF [auth T] Focus chain CK [auth y] Focus chain ED [auth C] Focus chain FD [auth C] Focus chain FI [auth c] Focus chain GH [auth b] Focus chain HH [auth b] Focus chain IH [auth b] Focus chain JJ [auth h] Focus chain KE [auth H] Focus chain LF [auth Y] Focus chain OI [auth c] Focus chain PJ [auth k] Focus chain QE [auth K] Focus chain TI [auth d] Focus chain VD [auth D] Focus chain VJ [auth t] Focus chain WA [auth A] Focus chain XB [auth B] Focus chain YB [auth B] Focus chain ZB [auth B] Interactions & Density Focus chain AG [auth a] Focus chain CF [auth T] Focus chain CK [auth y] Focus chain ED [auth C] Focus chain FD [auth C] Focus chain FI [auth c] Focus chain GH [auth b] Focus chain HH [auth b] Focus chain IH [auth b] Focus chain JJ [auth h] Focus chain KE [auth H] Focus chain LF [auth Y] Focus chain OI [auth c] Focus chain PJ [auth k] Focus chain QE [auth K] Focus chain TI [auth d] Focus chain VD [auth D] Focus chain VJ [auth t] Focus chain WA [auth A] Focus chain XB [auth B] Focus chain YB [auth B] Focus chain ZB [auth B]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain BC [auth B] SDF format, chain CB [auth A] SDF format, chain DF [auth T] SDF format, chain GG [auth a] SDF format, chain HE [auth F] SDF format, chain HJ [auth f] SDF format, chain KH [auth b] SDF format, chain LD [auth C] SDF format, chain OC [auth B] SDF format, chain RF [auth a] SDF format, chain SJ [auth m] SDF format, chain UE [auth M] SDF format, chain WE [auth M] SDF format, chain XE [auth M] MOL2 format, chain BC [auth B] MOL2 format, chain CB [auth A] MOL2 format, chain DF [auth T] MOL2 format, chain GG [auth a] MOL2 format, chain HE [auth F] MOL2 format, chain HJ [auth f] MOL2 format, chain KH [auth b] MOL2 format, chain LD [auth C] MOL2 format, chain OC [auth B] MOL2 format, chain RF [auth a] MOL2 format, chain SJ [auth m] MOL2 format, chain UE [auth M] MOL2 format, chain WE [auth M] MOL2 format, chain XE [auth M] mmCIF format, chain BC [auth B] mmCIF format, chain CB [auth A] mmCIF format, chain DF [auth T] mmCIF format, chain GG [auth a] mmCIF format, chain HE [auth F] mmCIF format, chain HJ [auth f] mmCIF format, chain KH [auth b] mmCIF format, chain LD [auth C] mmCIF format, chain OC [auth B] mmCIF format, chain RF [auth a] mmCIF format, chain SJ [auth m] mmCIF format, chain UE [auth M] mmCIF format, chain WE [auth M] mmCIF format, chain XE [auth M]	BC [auth B] CB [auth A] DF [auth T] GG [auth a] HE [auth F] BC [auth B], CB [auth A], DF [auth T], GG [auth a], HE [auth F], HJ [auth f], KH [auth b], LD [auth C], OC [auth B], RF [auth a], SJ [auth m], UE [auth M], WE [auth M], XE [auth M]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain BC [auth B] Focus chain CB [auth A] Focus chain DF [auth T] Focus chain GG [auth a] Focus chain HE [auth F] Focus chain HJ [auth f] Focus chain KH [auth b] Focus chain LD [auth C] Focus chain OC [auth B] Focus chain RF [auth a] Focus chain SJ [auth m] Focus chain UE [auth M] Focus chain WE [auth M] Focus chain XE [auth M] Interactions & Density Focus chain BC [auth B] Focus chain CB [auth A] Focus chain DF [auth T] Focus chain GG [auth a] Focus chain HE [auth F] Focus chain HJ [auth f] Focus chain KH [auth b] Focus chain LD [auth C] Focus chain OC [auth B] Focus chain RF [auth a] Focus chain SJ [auth m] Focus chain UE [auth M] Focus chain WE [auth M] Focus chain XE [auth M]
OEX Query on OEX Download Ideal Coordinates CCD File SDF format, chain DB [auth A] SDF format, chain EG [auth a] MOL2 format, chain DB [auth A] MOL2 format, chain EG [auth a] mmCIF format, chain DB [auth A] mmCIF format, chain EG [auth a]	DB [auth A], EG [auth a]	CA-MN4-O5 CLUSTER Ca Mn₄ O₅ SEXWDHMBWJEXOJ-UHFFFAOYSA-N		Interactions Focus chain DB [auth A] Focus chain EG [auth a] Interactions & Density Focus chain DB [auth A] Focus chain EG [auth a]
HTG Query on HTG Download Ideal Coordinates CCD File SDF format, chain AJ [auth d] SDF format, chain CC [auth B] SDF format, chain DC [auth B] SDF format, chain DE [auth D] SDF format, chain EC [auth B] SDF format, chain HG [auth b] SDF format, chain KF [auth V] SDF format, chain LC [auth B] SDF format, chain LH [auth b] SDF format, chain LI [auth c] SDF format, chain MC [auth B] SDF format, chain MD [auth C] SDF format, chain MH [auth b] SDF format, chain MI [auth c] SDF format, chain ND [auth C] SDF format, chain NG [auth b] SDF format, chain OG [auth b] MOL2 format, chain AJ [auth d] MOL2 format, chain CC [auth B] MOL2 format, chain DC [auth B] MOL2 format, chain DE [auth D] MOL2 format, chain EC [auth B] MOL2 format, chain HG [auth b] MOL2 format, chain KF [auth V] MOL2 format, chain LC [auth B] MOL2 format, chain LH [auth b] MOL2 format, chain LI [auth c] MOL2 format, chain MC [auth B] MOL2 format, chain MD [auth C] MOL2 format, chain MH [auth b] MOL2 format, chain MI [auth c] MOL2 format, chain ND [auth C] MOL2 format, chain NG [auth b] MOL2 format, chain OG [auth b] mmCIF format, chain AJ [auth d] mmCIF format, chain CC [auth B] mmCIF format, chain DC [auth B] mmCIF format, chain DE [auth D] mmCIF format, chain EC [auth B] mmCIF format, chain HG [auth b] mmCIF format, chain KF [auth V] mmCIF format, chain LC [auth B] mmCIF format, chain LH [auth b] mmCIF format, chain LI [auth c] mmCIF format, chain MC [auth B] mmCIF format, chain MD [auth C] mmCIF format, chain MH [auth b] mmCIF format, chain MI [auth c] mmCIF format, chain ND [auth C] mmCIF format, chain NG [auth b] mmCIF format, chain OG [auth b]	AJ [auth d] CC [auth B] DC [auth B] DE [auth D] EC [auth B] AJ [auth d], CC [auth B], DC [auth B], DE [auth D], EC [auth B], HG [auth b], KF [auth V], LC [auth B], LH [auth b], LI [auth c], MC [auth B], MD [auth C], MH [auth b], MI [auth c], ND [auth C], NG [auth b], OG [auth b]	heptyl 1-thio-beta-D-glucopyranoside C₁₃ H₂₆ O₅ S HPEGNLMTTNTJSP-LBELIVKGSA-N		Interactions Focus chain AJ [auth d] Focus chain CC [auth B] Focus chain DC [auth B] Focus chain DE [auth D] Focus chain EC [auth B] Focus chain HG [auth b] Focus chain KF [auth V] Focus chain LC [auth B] Focus chain LH [auth b] Focus chain LI [auth c] Focus chain MC [auth B] Focus chain MD [auth C] Focus chain MH [auth b] Focus chain MI [auth c] Focus chain ND [auth C] Focus chain NG [auth b] Focus chain OG [auth b] Interactions & Density Focus chain AJ [auth d] Focus chain CC [auth B] Focus chain DC [auth B] Focus chain DE [auth D] Focus chain EC [auth B] Focus chain HG [auth b] Focus chain KF [auth V] Focus chain LC [auth B] Focus chain LH [auth b] Focus chain LI [auth c] Focus chain MC [auth B] Focus chain MD [auth C] Focus chain MH [auth b] Focus chain MI [auth c] Focus chain ND [auth C] Focus chain NG [auth b] Focus chain OG [auth b]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain AF [auth T] SDF format, chain BF [auth T] SDF format, chain FC [auth B] SDF format, chain FF [auth V] SDF format, chain FJ [auth f] SDF format, chain GC [auth B] SDF format, chain GE [auth F] SDF format, chain GF [auth V] SDF format, chain HC [auth B] SDF format, chain HF [auth V] SDF format, chain IC [auth B] SDF format, chain IF [auth V] SDF format, chain IG [auth b] SDF format, chain JC [auth B] SDF format, chain JG [auth b] SDF format, chain KC [auth B] SDF format, chain KG [auth b] SDF format, chain LG [auth b] SDF format, chain MG [auth b] SDF format, chain OD [auth C] SDF format, chain OF [auth a] SDF format, chain OH [auth c] SDF format, chain PC [auth B] SDF format, chain PD [auth C] SDF format, chain PF [auth a] SDF format, chain PH [auth c] SDF format, chain TJ [auth o] SDF format, chain WJ [auth t] SDF format, chain XJ [auth v] SDF format, chain YA [auth A] SDF format, chain YE [auth O] SDF format, chain YJ [auth v] SDF format, chain ZA [auth A] SDF format, chain ZJ [auth v] MOL2 format, chain AB [auth A] MOL2 format, chain AF [auth T] MOL2 format, chain BF [auth T] MOL2 format, chain FC [auth B] MOL2 format, chain FF [auth V] MOL2 format, chain FJ [auth f] MOL2 format, chain GC [auth B] MOL2 format, chain GE [auth F] MOL2 format, chain GF [auth V] MOL2 format, chain HC [auth B] MOL2 format, chain HF [auth V] MOL2 format, chain IC [auth B] MOL2 format, chain IF [auth V] MOL2 format, chain IG [auth b] MOL2 format, chain JC [auth B] MOL2 format, chain JG [auth b] MOL2 format, chain KC [auth B] MOL2 format, chain KG [auth b] MOL2 format, chain LG [auth b] MOL2 format, chain MG [auth b] MOL2 format, chain OD [auth C] MOL2 format, chain OF [auth a] MOL2 format, chain OH [auth c] MOL2 format, chain PC [auth B] MOL2 format, chain PD [auth C] MOL2 format, chain PF [auth a] MOL2 format, chain PH [auth c] MOL2 format, chain TJ [auth o] MOL2 format, chain WJ [auth t] MOL2 format, chain XJ [auth v] MOL2 format, chain YA [auth A] MOL2 format, chain YE [auth O] MOL2 format, chain YJ [auth v] MOL2 format, chain ZA [auth A] MOL2 format, chain ZJ [auth v] mmCIF format, chain AB [auth A] mmCIF format, chain AF [auth T] mmCIF format, chain BF [auth T] mmCIF format, chain FC [auth B] mmCIF format, chain FF [auth V] mmCIF format, chain FJ [auth f] mmCIF format, chain GC [auth B] mmCIF format, chain GE [auth F] mmCIF format, chain GF [auth V] mmCIF format, chain HC [auth B] mmCIF format, chain HF [auth V] mmCIF format, chain IC [auth B] mmCIF format, chain IF [auth V] mmCIF format, chain IG [auth b] mmCIF format, chain JC [auth B] mmCIF format, chain JG [auth b] mmCIF format, chain KC [auth B] mmCIF format, chain KG [auth b] mmCIF format, chain LG [auth b] mmCIF format, chain MG [auth b] mmCIF format, chain OD [auth C] mmCIF format, chain OF [auth a] mmCIF format, chain OH [auth c] mmCIF format, chain PC [auth B] mmCIF format, chain PD [auth C] mmCIF format, chain PF [auth a] mmCIF format, chain PH [auth c] mmCIF format, chain TJ [auth o] mmCIF format, chain WJ [auth t] mmCIF format, chain XJ [auth v] mmCIF format, chain YA [auth A] mmCIF format, chain YE [auth O] mmCIF format, chain YJ [auth v] mmCIF format, chain ZA [auth A] mmCIF format, chain ZJ [auth v]	AB [auth A] AF [auth T] BF [auth T] FC [auth B] FF [auth V] AB [auth A], AF [auth T], BF [auth T], FC [auth B], FF [auth V], FJ [auth f], GC [auth B], GE [auth F], GF [auth V], HC [auth B], HF [auth V], IC [auth B], IF [auth V], IG [auth b], JC [auth B], JG [auth b], KC [auth B], KG [auth b], LG [auth b], MG [auth b], OD [auth C], OF [auth a], OH [auth c], PC [auth B], PD [auth C], PF [auth a], PH [auth c], TJ [auth o], WJ [auth t], XJ [auth v], YA [auth A], YE [auth O], YJ [auth v], ZA [auth A], ZJ [auth v]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth A] Focus chain AF [auth T] Focus chain BF [auth T] Focus chain FC [auth B] Focus chain FF [auth V] Focus chain FJ [auth f] Focus chain GC [auth B] Focus chain GE [auth F] Focus chain GF [auth V] Focus chain HC [auth B] Focus chain HF [auth V] Focus chain IC [auth B] Focus chain IF [auth V] Focus chain IG [auth b] Focus chain JC [auth B] Focus chain JG [auth b] Focus chain KC [auth B] Focus chain KG [auth b] Focus chain LG [auth b] Focus chain MG [auth b] Focus chain OD [auth C] Focus chain OF [auth a] Focus chain OH [auth c] Focus chain PC [auth B] Focus chain PD [auth C] Focus chain PF [auth a] Focus chain PH [auth c] Focus chain TJ [auth o] Focus chain WJ [auth t] Focus chain XJ [auth v] Focus chain YA [auth A] Focus chain YE [auth O] Focus chain YJ [auth v] Focus chain ZA [auth A] Focus chain ZJ [auth v] Interactions & Density Focus chain AB [auth A] Focus chain AF [auth T] Focus chain BF [auth T] Focus chain FC [auth B] Focus chain FF [auth V] Focus chain FJ [auth f] Focus chain GC [auth B] Focus chain GE [auth F] Focus chain GF [auth V] Focus chain HC [auth B] Focus chain HF [auth V] Focus chain IC [auth B] Focus chain IF [auth V] Focus chain IG [auth b] Focus chain JC [auth B] Focus chain JG [auth b] Focus chain KC [auth B] Focus chain KG [auth b] Focus chain LG [auth b] Focus chain MG [auth b] Focus chain OD [auth C] Focus chain OF [auth a] Focus chain OH [auth c] Focus chain PC [auth B] Focus chain PD [auth C] Focus chain PF [auth a] Focus chain PH [auth c] Focus chain TJ [auth o] Focus chain WJ [auth t] Focus chain XJ [auth v] Focus chain YA [auth A] Focus chain YE [auth O] Focus chain YJ [auth v] Focus chain ZA [auth A] Focus chain ZJ [auth v]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain FG [auth a] SDF format, chain QA [auth A] MOL2 format, chain FG [auth a] MOL2 format, chain QA [auth A] mmCIF format, chain FG [auth a] mmCIF format, chain QA [auth A]	FG [auth a], QA [auth A]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain FG [auth a] Focus chain QA [auth A] Interactions & Density Focus chain FG [auth a] Focus chain QA [auth A]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain NA [auth A] SDF format, chain TF [auth a] MOL2 format, chain NA [auth A] MOL2 format, chain TF [auth a] mmCIF format, chain NA [auth A] mmCIF format, chain TF [auth a]	NA [auth A], TF [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain NA [auth A] Focus chain TF [auth a] Interactions & Density Focus chain NA [auth A] Focus chain TF [auth a]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain GB [auth B] SDF format, chain IJ [auth f] SDF format, chain JE [auth F] SDF format, chain PG [auth b] SDF format, chain QD [auth C] SDF format, chain QH [auth c] SDF format, chain RH [auth c] SDF format, chain UJ [auth o] SDF format, chain ZE [auth O] MOL2 format, chain GB [auth B] MOL2 format, chain IJ [auth f] MOL2 format, chain JE [auth F] MOL2 format, chain PG [auth b] MOL2 format, chain QD [auth C] MOL2 format, chain QH [auth c] MOL2 format, chain RH [auth c] MOL2 format, chain UJ [auth o] MOL2 format, chain ZE [auth O] mmCIF format, chain GB [auth B] mmCIF format, chain IJ [auth f] mmCIF format, chain JE [auth F] mmCIF format, chain PG [auth b] mmCIF format, chain QD [auth C] mmCIF format, chain QH [auth c] mmCIF format, chain RH [auth c] mmCIF format, chain UJ [auth o] mmCIF format, chain ZE [auth O]	GB [auth B] IJ [auth f] JE [auth F] PG [auth b] QD [auth C] GB [auth B], IJ [auth f], JE [auth F], PG [auth b], QD [auth C], QH [auth c], RH [auth c], UJ [auth o], ZE [auth O]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain GB [auth B] Focus chain IJ [auth f] Focus chain JE [auth F] Focus chain PG [auth b] Focus chain QD [auth C] Focus chain QH [auth c] Focus chain RH [auth c] Focus chain UJ [auth o] Focus chain ZE [auth O] Interactions & Density Focus chain GB [auth B] Focus chain IJ [auth f] Focus chain JE [auth F] Focus chain PG [auth b] Focus chain QD [auth C] Focus chain QH [auth c] Focus chain RH [auth c] Focus chain UJ [auth o] Focus chain ZE [auth O]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AK [auth v] SDF format, chain EF [auth U] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain UF [auth a] SDF format, chain VF [auth a] MOL2 format, chain AK [auth v] MOL2 format, chain EF [auth U] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain UF [auth a] MOL2 format, chain VF [auth a] mmCIF format, chain AK [auth v] mmCIF format, chain EF [auth U] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain UF [auth a] mmCIF format, chain VF [auth a]	AK [auth v] EF [auth U] OA [auth A] PA [auth A] UF [auth a] AK [auth v], EF [auth U], OA [auth A], PA [auth A], UF [auth a], VF [auth a]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AK [auth v] Focus chain EF [auth U] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain UF [auth a] Focus chain VF [auth a] Interactions & Density Focus chain AK [auth v] Focus chain EF [auth U] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain UF [auth a] Focus chain VF [auth a]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain OJ [auth j] SDF format, chain PE [auth J] MOL2 format, chain OJ [auth j] MOL2 format, chain PE [auth J] mmCIF format, chain OJ [auth j] mmCIF format, chain PE [auth J]	OJ [auth j], PE [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain OJ [auth j] Focus chain PE [auth J] Interactions & Density Focus chain OJ [auth j] Focus chain PE [auth J]
UNL Query on UNL Download Ideal Coordinates CCD File	BE [auth D] BJ [auth d] CE [auth D] FB [auth A] LJ [auth i] BE [auth D], BJ [auth d], CE [auth D], FB [auth A], LJ [auth i], ME [auth I], MF [auth X], NC [auth B], NH [auth b], NI [auth c], NJ [auth j], OE [auth J], QF [auth a], RD [auth C], RJ [auth m], VE [auth M], YI [auth d], ZI [auth d]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BE [auth D] Focus chain BJ [auth d] Focus chain CE [auth D] Focus chain FB [auth A] Focus chain LJ [auth i] Focus chain ME [auth I] Focus chain MF [auth X] Focus chain NC [auth B] Focus chain NH [auth b] Focus chain NI [auth c] Focus chain NJ [auth j] Focus chain OE [auth J] Focus chain QF [auth a] Focus chain RD [auth C] Focus chain RJ [auth m] Focus chain VE [auth M] Focus chain YI [auth d] Focus chain ZI [auth d] Interactions & Density Focus chain BE [auth D] Focus chain BJ [auth d] Focus chain CE [auth D] Focus chain FB [auth A] Focus chain LJ [auth i] Focus chain ME [auth I] Focus chain MF [auth X] Focus chain NC [auth B] Focus chain NH [auth b] Focus chain NI [auth c] Focus chain NJ [auth j] Focus chain OE [auth J] Focus chain QF [auth a] Focus chain RD [auth C] Focus chain RJ [auth m] Focus chain VE [auth M] Focus chain YI [auth d] Focus chain ZI [auth d]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	BA [auth i], H [auth I]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 ?
R-Value Free: 0.198
R-Value Work: 0.152
R-Value Observed: 0.154
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 121.97	α = 90
b = 228.72	β = 90
c = 286.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-10-16

Deposition Author(s):

Suga, M.

Shen, J.R.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--

Revision History (Full details and data files)

Version 1.0: 2019-10-16
Type: Initial release
Version 1.1: 2019-10-30
Changes: Data collection, Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Derived calculations, Structure summary
Version 2.0: 2023-11-22
Changes: Advisory, Data collection, Database references, Non-polymer description, Refinement description, Structure summary
Version 2.1: 2024-10-30
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Help and Resources

6JLJ

XFEL structure of cyanobacterial photosystem II (dark state, dataset1)

An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser.

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