8RJA | pdb_00008rja

Crystal structure of the F420-reducing formylmethanofuran dehydrogenase complex from the ethanotroph Candidatus Ethanoperedens thermophilum

PDB DOI: https://doi.org/10.2210/pdb8RJA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candidatus Methanoperedenaceae archaeon GB50
Mutation(s): No

Deposited: 2023-12-20 Released: 2024-10-02
Deposition Author(s): Lemaire, O.N., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 ?
R-Value Free:
0.210 (Depositor), 0.212 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

F420 reduction as a cellular driver for anaerobic ethanotrophy

Lemaire, O.N., Wegener, G., Wagner, T.

To be published.

Macromolecule Content

Total Structure Weight: 412.54 kDa
Atom Count: 30,528
Modelled Residue Count: 3,602
Deposited Residue Count: 3,640
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formylmethanofuran dehydrogenase subunit A	A, G	567	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0 EC: 3.5.2.5
UniProt
Find proteins for A0A7R9MYH2 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9MYH2 Go to UniProtKB: A0A7R9MYH2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9MYH2
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Formylmethanofuran dehydrogenase subunit B	B, H	430	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0
UniProt
Find proteins for A0A7R9R4U5 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9R4U5 Go to UniProtKB: A0A7R9R4U5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9R4U5
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
formylmethanofuran dehydrogenase	C, I	253	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0 EC: 1.2.7.12
UniProt
Find proteins for A0A7R9MYM1 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9MYM1 Go to UniProtKB: A0A7R9MYM1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9MYM1
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Formylmethanofuran dehydrogenase subunit D	D, J	126	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0 EC: 1.2.7.12
UniProt
Find proteins for A0A7R9R4V6 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9R4V6 Go to UniProtKB: A0A7R9R4V6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9R4V6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus	E, K	359	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0
UniProt
Find proteins for A0A7R9N9K9 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9N9K9 Go to UniProtKB: A0A7R9N9K9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9N9K9
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-quinone oxidoreductase subunit I, chloroplastic	F, L	85	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0 EC: 1.6.5.11
UniProt
Find proteins for A0A7R9MZV2 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9MZV2 Go to UniProtKB: A0A7R9MZV2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9MZV2
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Reference Sequence

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain TB [auth K] MOL2 format, chain JA [auth E] MOL2 format, chain TB [auth K] mmCIF format, chain JA [auth E] mmCIF format, chain TB [auth K]	JA [auth E], TB [auth K]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain JA [auth E] Focus chain TB [auth K] Interactions & Density Focus chain JA [auth E] Focus chain TB [auth K]
MGD (Subject of Investigation/LOI) Query on MGD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain DB [auth H] SDF format, chain EB [auth H] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DB [auth H] MOL2 format, chain EB [auth H] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DB [auth H] mmCIF format, chain EB [auth H]	AA [auth B], BA [auth B], DB [auth H], EB [auth H]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DB [auth H] Focus chain EB [auth H] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DB [auth H] Focus chain EB [auth H]
PE4 Query on PE4 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain PB [auth I] SDF format, chain R [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain PB [auth I] MOL2 format, chain R [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain PB [auth I] mmCIF format, chain R [auth A]	EA [auth B], PB [auth I], R [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain PB [auth I] Focus chain R [auth A] Interactions & Density Focus chain EA [auth B] Focus chain PB [auth I] Focus chain R [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain BB [auth H] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain KA [auth E] SDF format, chain RA [auth F] SDF format, chain RB [auth K] SDF format, chain SA [auth F] SDF format, chain SB [auth K] SDF format, chain UB [auth K] SDF format, chain Y [auth B] SDF format, chain YB [auth L] SDF format, chain ZB [auth L] MOL2 format, chain BB [auth H] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain RA [auth F] MOL2 format, chain RB [auth K] MOL2 format, chain SA [auth F] MOL2 format, chain SB [auth K] MOL2 format, chain UB [auth K] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth L] MOL2 format, chain ZB [auth L] mmCIF format, chain BB [auth H] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain RA [auth F] mmCIF format, chain RB [auth K] mmCIF format, chain SA [auth F] mmCIF format, chain SB [auth K] mmCIF format, chain UB [auth K] mmCIF format, chain Y [auth B] mmCIF format, chain YB [auth L] mmCIF format, chain ZB [auth L]	BB [auth H] HA [auth E] IA [auth E] KA [auth E] RA [auth F] BB [auth H], HA [auth E], IA [auth E], KA [auth E], RA [auth F], RB [auth K], SA [auth F], SB [auth K], UB [auth K], Y [auth B], YB [auth L], ZB [auth L]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain BB [auth H] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain KA [auth E] Focus chain RA [auth F] Focus chain RB [auth K] Focus chain SA [auth F] Focus chain SB [auth K] Focus chain UB [auth K] Focus chain Y [auth B] Focus chain YB [auth L] Focus chain ZB [auth L] Interactions & Density Focus chain BB [auth H] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain KA [auth E] Focus chain RA [auth F] Focus chain RB [auth K] Focus chain SA [auth F] Focus chain SB [auth K] Focus chain UB [auth K] Focus chain Y [auth B] Focus chain YB [auth L] Focus chain ZB [auth L]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain NB [auth I] MOL2 format, chain NB [auth I] mmCIF format, chain NB [auth I]	NB [auth I]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain NB [auth I] Interactions & Density Focus chain NB [auth I]
W (Subject of Investigation/LOI) Query on W Download Ideal Coordinates CCD File SDF format, chain CB [auth H] SDF format, chain Z [auth B] MOL2 format, chain CB [auth H] MOL2 format, chain Z [auth B] mmCIF format, chain CB [auth H] mmCIF format, chain Z [auth B]	CB [auth H], Z [auth B]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain CB [auth H] Focus chain Z [auth B] Interactions & Density Focus chain CB [auth H] Focus chain Z [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FB [auth H] SDF format, chain IB [auth H] SDF format, chain JB [auth H] SDF format, chain LA [auth E] SDF format, chain MB [auth I] SDF format, chain OB [auth I] SDF format, chain P [auth A] SDF format, chain T [auth A] SDF format, chain W [auth A] MOL2 format, chain FB [auth H] MOL2 format, chain IB [auth H] MOL2 format, chain JB [auth H] MOL2 format, chain LA [auth E] MOL2 format, chain MB [auth I] MOL2 format, chain OB [auth I] MOL2 format, chain P [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth A] mmCIF format, chain FB [auth H] mmCIF format, chain IB [auth H] mmCIF format, chain JB [auth H] mmCIF format, chain LA [auth E] mmCIF format, chain MB [auth I] mmCIF format, chain OB [auth I] mmCIF format, chain P [auth A] mmCIF format, chain T [auth A] mmCIF format, chain W [auth A]	FB [auth H] IB [auth H] JB [auth H] LA [auth E] MB [auth I] FB [auth H], IB [auth H], JB [auth H], LA [auth E], MB [auth I], OB [auth I], P [auth A], T [auth A], W [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FB [auth H] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain LA [auth E] Focus chain MB [auth I] Focus chain OB [auth I] Focus chain P [auth A] Focus chain T [auth A] Focus chain W [auth A] Interactions & Density Focus chain FB [auth H] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain LA [auth E] Focus chain MB [auth I] Focus chain OB [auth I] Focus chain P [auth A] Focus chain T [auth A] Focus chain W [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain UA [auth G] SDF format, chain VA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth G]	M [auth A], N [auth A], UA [auth G], VA [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain UA [auth G] Focus chain VA [auth G] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain UA [auth G] Focus chain VA [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain FA [auth B] SDF format, chain KB [auth H] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VB [auth K] SDF format, chain WB [auth K] SDF format, chain XA [auth G] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain AB [auth G] MOL2 format, chain FA [auth B] MOL2 format, chain KB [auth H] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth K] MOL2 format, chain WB [auth K] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G] mmCIF format, chain AB [auth G] mmCIF format, chain FA [auth B] mmCIF format, chain KB [auth H] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth K] mmCIF format, chain WB [auth K] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain ZA [auth G]	AB [auth G] FA [auth B] KB [auth H] MA [auth E] NA [auth E] AB [auth G], FA [auth B], KB [auth H], MA [auth E], NA [auth E], OA [auth E], PA [auth E], U [auth A], V [auth A], VB [auth K], WB [auth K], XA [auth G], YA [auth G], ZA [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain FA [auth B] Focus chain KB [auth H] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain U [auth A] Focus chain V [auth A] Focus chain VB [auth K] Focus chain WB [auth K] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain FA [auth B] Focus chain KB [auth H] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain U [auth A] Focus chain V [auth A] Focus chain VB [auth K] Focus chain WB [auth K] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain HB [auth H] SDF format, chain Q [auth A] SDF format, chain QB [auth I] SDF format, chain S [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain HB [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth I] MOL2 format, chain S [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain HB [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth I] mmCIF format, chain S [auth A]	DA [auth B], HB [auth H], Q [auth A], QB [auth I], S [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain HB [auth H] Focus chain Q [auth A] Focus chain QB [auth I] Focus chain S [auth A] Interactions & Density Focus chain DA [auth B] Focus chain HB [auth H] Focus chain Q [auth A] Focus chain QB [auth I] Focus chain S [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AC [auth L] SDF format, chain GA [auth C] SDF format, chain TA [auth F] SDF format, chain X [auth A] MOL2 format, chain AC [auth L] MOL2 format, chain GA [auth C] MOL2 format, chain TA [auth F] MOL2 format, chain X [auth A] mmCIF format, chain AC [auth L] mmCIF format, chain GA [auth C] mmCIF format, chain TA [auth F] mmCIF format, chain X [auth A]	AC [auth L], GA [auth C], TA [auth F], X [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AC [auth L] Focus chain GA [auth C] Focus chain TA [auth F] Focus chain X [auth A] Interactions & Density Focus chain AC [auth L] Focus chain GA [auth C] Focus chain TA [auth F] Focus chain X [auth A]
H2S (Subject of Investigation/LOI) Query on H2S Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain GB [auth H] MOL2 format, chain CA [auth B] MOL2 format, chain GB [auth H] mmCIF format, chain CA [auth B] mmCIF format, chain GB [auth H]	CA [auth B], GB [auth H]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain GB [auth H] Interactions & Density Focus chain CA [auth B] Focus chain GB [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain LB [auth H] SDF format, chain QA [auth E] SDF format, chain WA [auth G] SDF format, chain XB [auth K] MOL2 format, chain LB [auth H] MOL2 format, chain QA [auth E] MOL2 format, chain WA [auth G] MOL2 format, chain XB [auth K] mmCIF format, chain LB [auth H] mmCIF format, chain QA [auth E] mmCIF format, chain WA [auth G] mmCIF format, chain XB [auth K]	LB [auth H], QA [auth E], WA [auth G], XB [auth K]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain LB [auth H] Focus chain QA [auth E] Focus chain WA [auth G] Focus chain XB [auth K] Interactions & Density Focus chain LB [auth H] Focus chain QA [auth E] Focus chain WA [auth G] Focus chain XB [auth K]