9FSV

Yeast 20S proteasome with human beta2i (1-53) in complex with epoxyketone inhibitor 42

PDB DOI: https://doi.org/10.2210/pdb9FSV/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae, Homo sapiens
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2024-06-22 Released: 2024-07-17
Deposition Author(s): Maurits, E., Huber, E.M., Dekker, P.M., Wang, X., Heinemeyer, W., Florea, B.I., Groll, M., Overkleeft, H.S.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.247
R-Value Work: 0.213
R-Value Observed: 0.215

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-based design of peptide epoxyketones selectively targeting the three human immunoproteasome active sites

Maurits, E., Huber, E.M., Dekker, P.M., Wang, X., Heinemeyer, W., Florea, B.I., Groll, M., Overkleeft, H.S.

To be published.

Macromolecule Content

Total Structure Weight: 733.65 kDa
Atom Count: 49,917
Modelled Residue Count: 6,337
Deposited Residue Count: 6,598
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, O	250	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639 Go to UniProtKB: P23639
Entity Groups
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, P	258	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638 Go to UniProtKB: P23638
Entity Groups
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, Q	254	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303 Go to UniProtKB: P40303
Entity Groups
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, 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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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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, S	234	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302 Go to UniProtKB: P40302
Entity Groups
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, T	288	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242 Go to UniProtKB: P21242
Entity Groups
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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, 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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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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-10,Proteasome subunit beta type-2	H, V	225	Homo sapiens, Saccharomyces cerevisiae This entity is chimeric	Mutation(s): 0 Gene Names: PSMB10, LMP10, MECL1, PUP1, YOR157C EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25043 Go to UniProtKB: P25043
Find proteins for P40306 (Homo sapiens) Explore P40306 Go to UniProtKB: P40306
PHAROS: P40306 GTEx: ENSG00000205220
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P40306P25043
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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	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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UniProt Group	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	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	K, Y	211	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	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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], M	246	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30657 Go to UniProtKB: P30657
Entity Groups
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], 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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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38624
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Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IFL (Subject of Investigation/LOI) Query on A1IFL Download Ideal Coordinates CCD File SDF format, chain FA [auth H] SDF format, chain KA [auth K] SDF format, chain RA [auth V] SDF format, chain WA [auth Y] MOL2 format, chain FA [auth H] MOL2 format, chain KA [auth K] MOL2 format, chain RA [auth V] MOL2 format, chain WA [auth Y] mmCIF format, chain FA [auth H] mmCIF format, chain KA [auth K] mmCIF format, chain RA [auth V] mmCIF format, chain WA [auth Y]	FA [auth H], KA [auth K], RA [auth V], WA [auth Y]	(2S)-N-[(2S)-1-[[(1S)-2-cyclohexyl-1-[(2R,3S,6R,7S)-3-methanoyl-2,6-dimethyl-6,7-bis(oxidanyl)-1,4-oxazepan-7-yl]ethyl]amino]-3-(4-methoxyphenyl)-1-oxidanylidene-propan-2-yl]-2-(2-morpholin-4-ylethanoylamino)-4-oxidanyl-butanamide C₃₆ H₅₇ N₅ O₁₀ QYIOHDOWDBWIOM-HFFQPBMXSA-N		Interactions Focus chain FA [auth H] Focus chain KA [auth K] Focus chain RA [auth V] Focus chain WA [auth Y] Interactions & Density Focus chain FA [auth H] Focus chain KA [auth K] Focus chain RA [auth V] Focus chain WA [auth Y]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain IA [auth K] SDF format, chain QA [auth V] SDF format, chain UA [auth Y] MOL2 format, chain EA [auth H] MOL2 format, chain IA [auth K] MOL2 format, chain QA [auth V] MOL2 format, chain UA [auth Y] mmCIF format, chain EA [auth H] mmCIF format, chain IA [auth K] mmCIF format, chain QA [auth V] mmCIF format, chain UA [auth Y]	EA [auth H], IA [auth K], QA [auth V], UA [auth Y]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain EA [auth H] Focus chain IA [auth K] Focus chain QA [auth V] Focus chain UA [auth Y] Interactions & Density Focus chain EA [auth H] Focus chain IA [auth K] Focus chain QA [auth V] Focus chain UA [auth Y]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth K] SDF format, chain MA [auth N] SDF format, chain VA [auth Y] SDF format, chain YA [auth b] MOL2 format, chain JA [auth K] MOL2 format, chain MA [auth N] MOL2 format, chain VA [auth Y] MOL2 format, chain YA [auth b] mmCIF format, chain JA [auth K] mmCIF format, chain MA [auth N] mmCIF format, chain VA [auth Y] mmCIF format, chain YA [auth b]	JA [auth K], MA [auth N], VA [auth Y], YA [auth b]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain JA [auth K] Focus chain MA [auth N] Focus chain VA [auth Y] Focus chain YA [auth b] Interactions & Density Focus chain JA [auth K] Focus chain MA [auth N] Focus chain VA [auth Y] Focus chain YA [auth b]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain NA [auth N] SDF format, chain OA [auth U] MOL2 format, chain DA [auth G] MOL2 format, chain NA [auth N] MOL2 format, chain OA [auth U] mmCIF format, chain DA [auth G] mmCIF format, chain NA [auth N] mmCIF format, chain OA [auth U]	DA [auth G], NA [auth N], OA [auth U]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth G] Focus chain NA [auth N] Focus chain OA [auth U] Interactions & Density Focus chain DA [auth G] Focus chain NA [auth N] Focus chain OA [auth U]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain GA [auth I] SDF format, chain HA [auth K] SDF format, chain LA [auth N] SDF format, chain PA [auth V] SDF format, chain SA [auth W] SDF format, chain TA [auth Y] SDF format, chain XA [auth Z] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth K] MOL2 format, chain LA [auth N] MOL2 format, chain PA [auth V] MOL2 format, chain SA [auth W] MOL2 format, chain TA [auth Y] MOL2 format, chain XA [auth Z] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth K] mmCIF format, chain LA [auth N] mmCIF format, chain PA [auth V] mmCIF format, chain SA [auth W] mmCIF format, chain TA [auth Y] mmCIF format, chain XA [auth Z]	CA [auth G] GA [auth I] HA [auth K] LA [auth N] PA [auth V] CA [auth G], GA [auth I], HA [auth K], LA [auth N], PA [auth V], SA [auth W], TA [auth Y], XA [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain GA [auth I] Focus chain HA [auth K] Focus chain LA [auth N] Focus chain PA [auth V] Focus chain SA [auth W] Focus chain TA [auth Y] Focus chain XA [auth Z] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth I] Focus chain HA [auth K] Focus chain LA [auth N] Focus chain PA [auth V] Focus chain SA [auth W] Focus chain TA [auth Y] Focus chain XA [auth Z]