9AW6 | pdb_00009aw6

Yeast 20S proteasome soaked with MA9 fraction EF2

PDB DOI: https://doi.org/10.2210/pdb9AW6/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2024-03-05 Released: 2025-03-19
Deposition Author(s): Meneghello, R., Rustiguel, J.K., Fernandes, A.Z.N., Trivella, D.B.B.
Funding Organization(s): Other private, Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.44 ?
R-Value Free:
0.235 (Depositor), 0.236 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

High-throughput protein crystallography to empower natural product-based drug discovery

Meneghello, R., Rustiguel, J.K., Araujo, E.A., Felicio, R., Fernandes, A.Z.N., Ferreira, E.L.F., Gubiani, J.R., Takeda, A.A.S., Souza, A.A., Silva, C.C.L., Bertonha, A.F., Trindade, D.M., Cunha, T.M., Cardoso, A.C., Dessen, A., Berlinck, R.G.S., Nascimento, Z.F.Z., Trivella, D.B.B.

To be published.

Macromolecule Content

Total Structure Weight: 738.04 kDa
Atom Count: 50,447
Modelled Residue Count: 6,363
Deposited Residue Count: 6,586
Unique protein chains: 14

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	A, H [auth O]	250	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639 Go to UniProtKB: P23639
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23639
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	B, I [auth P]	258	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638 Go to UniProtKB: P23638
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23638
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	C, J [auth Q]	254	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303 Go to UniProtKB: P40303
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40303
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	D, K [auth R]	260	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32379 Go to UniProtKB: P32379
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UniProt Group	P32379
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	E, L [auth S]	234	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302 Go to UniProtKB: P40302
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40302
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable proteasome subunit alpha type-7	F, M [auth T]	287	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242 Go to UniProtKB: P21242
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UniProt Group	P21242
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	G, N [auth U]	252	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21243 Go to UniProtKB: P21243
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UniProt Group	P21243
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	O [auth H], V	232	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25043 Go to UniProtKB: P25043
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UniProt Group	P25043
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	P [auth I], W	205	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25451 Go to UniProtKB: P25451
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	Q [auth J], X	198	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22141 Go to UniProtKB: P22141
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UniProt Group	P22141
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	R [auth K], Y	212	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30656 Go to UniProtKB: P30656
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UniProt Group	P30656
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	S [auth L], Z	222	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23724 Go to UniProtKB: P23724
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UniProt Group	P23724
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	AA [auth a], T [auth M]	233	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30657 Go to UniProtKB: P30657
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30657
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	BA [auth b], U [auth N]	196	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38624 Go to UniProtKB: P38624
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UniProt Group	P38624
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A9B (Subject of Investigation/LOI) Query on A1A9B Download Ideal Coordinates CCD File SDF format, chain BC [auth Y] SDF format, chain EB [auth K] SDF format, chain UB [auth N] SDF format, chain VA [auth H] SDF format, chain VB [auth V] SDF format, chain PC [auth b] MOL2 format, chain BC [auth Y] MOL2 format, chain EB [auth K] MOL2 format, chain UB [auth N] MOL2 format, chain VA [auth H] MOL2 format, chain VB [auth V] MOL2 format, chain PC [auth b] mmCIF format, chain BC [auth Y] mmCIF format, chain EB [auth K] mmCIF format, chain UB [auth N] mmCIF format, chain VA [auth H] mmCIF format, chain VB [auth V] mmCIF format, chain PC [auth b]	BC [auth Y] EB [auth K] PC [auth b] UB [auth N] VA [auth H] BC [auth Y], EB [auth K], PC [auth b], UB [auth N], VA [auth H], VB [auth V]	(10S,11R,12S,15S,18S)-15-(2-amino-2-oxoethyl)-10,11,23-trihydroxy-18-{[(3R)-3-methyl-2-oxopentanoyl]amino}-9,14,17-trioxo-N-[(1Z)-prop-1-en-1-yl]-8,13,16-triazatetracyclo[18.3.1.0(2,7).0(6,10)]tetracosa-1(24),2,4,6,20,22-hexaene-12-carboxamide C₃₃ H₃₈ N₆ O₁₀ ZIAXNZCTODBCKW-NKGUOCGVSA-N		Interactions Focus chain BC [auth Y] Focus chain EB [auth K] Focus chain PC [auth b] Focus chain UB [auth N] Focus chain VA [auth H] Focus chain VB [auth V] Interactions & Density Focus chain BC [auth Y] Focus chain EB [auth K] Focus chain PC [auth b] Focus chain UB [auth N] Focus chain VA [auth H] Focus chain VB [auth V]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain AC [auth X] SDF format, chain BB [auth I] SDF format, chain CA [auth B] SDF format, chain CB [auth J] SDF format, chain DA [auth C] SDF format, chain DB [auth J] SDF format, chain DC [auth Y] SDF format, chain EA [auth D] SDF format, chain EC [auth Y] SDF format, chain FA [auth E] SDF format, chain FB [auth K] SDF format, chain FC [auth Y] SDF format, chain GA [auth E] SDF format, chain GB [auth K] SDF format, chain GC [auth Y] SDF format, chain HA [auth F] SDF format, chain HB [auth K] SDF format, chain IA [auth F] SDF format, chain IB [auth K] SDF format, chain IC [auth Z] SDF format, chain JA [auth G] SDF format, chain JC [auth Z] SDF format, chain KB [auth L] SDF format, chain KC [auth a] SDF format, chain LA [auth P] SDF format, chain LB [auth M] SDF format, chain LC [auth a] SDF format, chain MA [auth Q] SDF format, chain MB [auth M] SDF format, chain MC [auth a] SDF format, chain NA [auth S] SDF format, chain NB [auth M] SDF format, chain NC [auth a] SDF format, chain OA [auth S] SDF format, chain OB [auth M] SDF format, chain OC [auth a] SDF format, chain PA [auth S] SDF format, chain PB [auth M] SDF format, chain QA [auth T] SDF format, chain QB [auth M] SDF format, chain QC [auth b] SDF format, chain RA [auth T] SDF format, chain RB [auth M] SDF format, chain RC [auth b] SDF format, chain SA [auth T] SDF format, chain SB [auth M] SDF format, chain SC [auth b] SDF format, chain TA [auth U] SDF format, chain TB [auth N] SDF format, chain UA [auth U] SDF format, chain WA [auth H] SDF format, chain WB [auth V] SDF format, chain XA [auth H] SDF format, chain XB [auth V] SDF format, chain YA [auth H] SDF format, chain ZB [auth W] SDF format, chain KA [auth G] MOL2 format, chain AB [auth I] MOL2 format, chain AC [auth X] MOL2 format, chain BB [auth I] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth J] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth J] MOL2 format, chain DC [auth Y] MOL2 format, chain EA [auth D] MOL2 format, chain EC [auth Y] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth K] MOL2 format, chain FC [auth Y] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth K] MOL2 format, chain GC [auth Y] MOL2 format, chain HA [auth F] MOL2 format, chain HB [auth K] MOL2 format, chain IA [auth F] MOL2 format, chain IB [auth K] MOL2 format, chain IC [auth Z] MOL2 format, chain JA [auth G] MOL2 format, chain JC [auth Z] MOL2 format, chain KB [auth L] MOL2 format, chain KC [auth a] MOL2 format, chain LA [auth P] MOL2 format, chain LB [auth M] MOL2 format, chain LC [auth a] MOL2 format, chain MA [auth Q] MOL2 format, chain MB [auth M] MOL2 format, chain MC [auth a] MOL2 format, chain NA [auth S] MOL2 format, chain NB [auth M] MOL2 format, chain NC [auth a] MOL2 format, chain OA [auth S] MOL2 format, chain OB [auth M] MOL2 format, chain OC [auth a] MOL2 format, chain PA [auth S] MOL2 format, chain PB [auth M] MOL2 format, chain QA [auth T] MOL2 format, chain QB [auth M] MOL2 format, chain QC [auth b] MOL2 format, chain RA [auth T] MOL2 format, chain RB [auth M] MOL2 format, chain RC [auth b] MOL2 format, chain SA [auth T] MOL2 format, chain SB [auth M] MOL2 format, chain SC [auth b] MOL2 format, chain TA [auth U] MOL2 format, chain TB [auth N] MOL2 format, chain UA [auth U] MOL2 format, chain WA [auth H] MOL2 format, chain WB [auth V] MOL2 format, chain XA [auth H] MOL2 format, chain XB [auth V] MOL2 format, chain YA [auth H] MOL2 format, chain ZB [auth W] MOL2 format, chain KA [auth G] mmCIF format, chain AB [auth I] mmCIF format, chain AC [auth X] mmCIF format, chain BB [auth I] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth J] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth J] mmCIF format, chain DC [auth Y] mmCIF format, chain EA [auth D] mmCIF format, chain EC [auth Y] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth K] mmCIF format, chain FC [auth Y] mmCIF format, chain GA [auth E] mmCIF format, chain GB [auth K] mmCIF format, chain GC [auth Y] mmCIF format, chain HA [auth F] mmCIF format, chain HB [auth K] mmCIF format, chain IA [auth F] mmCIF format, chain IB [auth K] mmCIF format, chain IC [auth Z] mmCIF format, chain JA [auth G] mmCIF format, chain JC [auth Z] mmCIF format, chain KB [auth L] mmCIF format, chain KC [auth a] mmCIF format, chain LA [auth P] mmCIF format, chain LB [auth M] mmCIF format, chain LC [auth a] mmCIF format, chain MA [auth Q] mmCIF format, chain MB [auth M] mmCIF format, chain MC [auth a] mmCIF format, chain NA [auth S] mmCIF format, chain NB [auth M] mmCIF format, chain NC [auth a] mmCIF format, chain OA [auth S] mmCIF format, chain OB [auth M] mmCIF format, chain OC [auth a] mmCIF format, chain PA [auth S] mmCIF format, chain PB [auth M] mmCIF format, chain QA [auth T] mmCIF format, chain QB [auth M] mmCIF format, chain QC [auth b] mmCIF format, chain RA [auth T] mmCIF format, chain RB [auth M] mmCIF format, chain RC [auth b] mmCIF format, chain SA [auth T] mmCIF format, chain SB [auth M] mmCIF format, chain SC [auth b] mmCIF format, chain TA [auth U] mmCIF format, chain TB [auth N] mmCIF format, chain UA [auth U] mmCIF format, chain WA [auth H] mmCIF format, chain WB [auth V] mmCIF format, chain XA [auth H] mmCIF format, chain XB [auth V] mmCIF format, chain YA [auth H] mmCIF format, chain ZB [auth W] mmCIF format, chain KA [auth G]	AB [auth I] AC [auth X] BB [auth I] CA [auth B] CB [auth J] AB [auth I], AC [auth X], BB [auth I], CA [auth B], CB [auth J], DA [auth C], DB [auth J], DC [auth Y], EA [auth D], EC [auth Y], FA [auth E], FB [auth K], FC [auth Y], GA [auth E], GB [auth K], GC [auth Y], HA [auth F], HB [auth K], IA [auth F], IB [auth K], IC [auth Z], JA [auth G], JC [auth Z], KA [auth G], KB [auth L], KC [auth a], LA [auth P], LB [auth M], LC [auth a], MA [auth Q], MB [auth M], MC [auth a], NA [auth S], NB [auth M], NC [auth a], OA [auth S], OB [auth M], OC [auth a], PA [auth S], PB [auth M], QA [auth T], QB [auth M], QC [auth b], RA [auth T], RB [auth M], RC [auth b], SA [auth T], SB [auth M], SC [auth b], TA [auth U], TB [auth N], UA [auth U], WA [auth H], WB [auth V], XA [auth H], XB [auth V], YA [auth H], ZB [auth W]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth I] Focus chain AC [auth X] Focus chain BB [auth I] Focus chain CA [auth B] Focus chain CB [auth J] Focus chain DA [auth C] Focus chain DB [auth J] Focus chain DC [auth Y] Focus chain EA [auth D] Focus chain EC [auth Y] Focus chain FA [auth E] Focus chain FB [auth K] Focus chain FC [auth Y] Focus chain GA [auth E] Focus chain GB [auth K] Focus chain GC [auth Y] Focus chain HA [auth F] Focus chain HB [auth K] Focus chain IA [auth F] Focus chain IB [auth K] Focus chain IC [auth Z] Focus chain JA [auth G] Focus chain JC [auth Z] Focus chain KA [auth G] Focus chain KB [auth L] Focus chain KC [auth a] Focus chain LA [auth P] Focus chain LB [auth M] Focus chain LC [auth a] Focus chain MA [auth Q] Focus chain MB [auth M] Focus chain MC [auth a] Focus chain NA [auth S] Focus chain NB [auth M] Focus chain NC [auth a] Focus chain OA [auth S] Focus chain OB [auth M] Focus chain OC [auth a] Focus chain PA [auth S] Focus chain PB [auth M] Focus chain QA [auth T] Focus chain QB [auth M] Focus chain QC [auth b] Focus chain RA [auth T] Focus chain RB [auth M] Focus chain RC [auth b] Focus chain SA [auth T] Focus chain SB [auth M] Focus chain SC [auth b] Focus chain TA [auth U] Focus chain TB [auth N] Focus chain UA [auth U] Focus chain WA [auth H] Focus chain WB [auth V] Focus chain XA [auth H] Focus chain XB [auth V] Focus chain YA [auth H] Focus chain ZB [auth W] Interactions & Density Focus chain AB [auth I] Focus chain AC [auth X] Focus chain BB [auth I] Focus chain CA [auth B] Focus chain CB [auth J] Focus chain DA [auth C] Focus chain DB [auth J] Focus chain DC [auth Y] Focus chain EA [auth D] Focus chain EC [auth Y] Focus chain FA [auth E] Focus chain FB [auth K] Focus chain FC [auth Y] Focus chain GA [auth E] Focus chain GB [auth K] Focus chain GC [auth Y] Focus chain HA [auth F] Focus chain HB [auth K] Focus chain IA [auth F] Focus chain IB [auth K] Focus chain IC [auth Z] Focus chain JA [auth G] Focus chain JC [auth Z] Focus chain KA [auth G] Focus chain KB [auth L] Focus chain KC [auth a] Focus chain LA [auth P] Focus chain LB [auth M] Focus chain LC [auth a] Focus chain MA [auth Q] Focus chain MB [auth M] Focus chain MC [auth a] Focus chain NA [auth S] Focus chain NB [auth M] Focus chain NC [auth a] Focus chain OA [auth S] Focus chain OB [auth M] Focus chain OC [auth a] Focus chain PA [auth S] Focus chain PB [auth M] Focus chain QA [auth T] Focus chain QB [auth M] Focus chain QC [auth b] Focus chain RA [auth T] Focus chain RB [auth M] Focus chain RC [auth b] Focus chain SA [auth T] Focus chain SB [auth M] Focus chain SC [auth b] Focus chain TA [auth U] Focus chain TB [auth N] Focus chain UA [auth U] Focus chain WA [auth H] Focus chain WB [auth V] Focus chain XA [auth H] Focus chain XB [auth V] Focus chain YA [auth H] Focus chain ZB [auth W]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CC [auth Y] SDF format, chain HC [auth Z] SDF format, chain JB [auth L] SDF format, chain YB [auth W] SDF format, chain ZA [auth I] MOL2 format, chain CC [auth Y] MOL2 format, chain HC [auth Z] MOL2 format, chain JB [auth L] MOL2 format, chain YB [auth W] MOL2 format, chain ZA [auth I] mmCIF format, chain CC [auth Y] mmCIF format, chain HC [auth Z] mmCIF format, chain JB [auth L] mmCIF format, chain YB [auth W] mmCIF format, chain ZA [auth I]	CC [auth Y], HC [auth Z], JB [auth L], YB [auth W], ZA [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CC [auth Y] Focus chain HC [auth Z] Focus chain JB [auth L] Focus chain YB [auth W] Focus chain ZA [auth I] Interactions & Density Focus chain CC [auth Y] Focus chain HC [auth Z] Focus chain JB [auth L] Focus chain YB [auth W] Focus chain ZA [auth I]