9FT0

Yeast 20S proteasome in complex with epoxyketone inhibitor 42

PDB DOI: https://doi.org/10.2210/pdb9FT0/pdb

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

Deposited: 2024-06-23 Released: 2024-07-10
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: 0.232
R-Value Work: 0.190
R-Value Observed: 0.193

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

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: 734.8 kDa
Atom Count: 49,929
Modelled Residue Count: 6,364
Deposited Residue Count: 6,610
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
Entity Groups
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
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
Entity Groups
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-2	H, V	231	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
Entity Groups
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 XA [auth Y] MOL2 format, chain FA [auth H] MOL2 format, chain KA [auth K] MOL2 format, chain RA [auth V] MOL2 format, chain XA [auth Y] mmCIF format, chain FA [auth H] mmCIF format, chain KA [auth K] mmCIF format, chain RA [auth V] mmCIF format, chain XA [auth Y]	FA [auth H], KA [auth K], RA [auth V], XA [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 XA [auth Y] Interactions & Density Focus chain FA [auth H] Focus chain KA [auth K] Focus chain RA [auth V] Focus chain XA [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 UA [auth X] MOL2 format, chain EA [auth H] MOL2 format, chain IA [auth K] MOL2 format, chain UA [auth X] mmCIF format, chain EA [auth H] mmCIF format, chain IA [auth K] mmCIF format, chain UA [auth X]	EA [auth H], IA [auth K], UA [auth X]	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 UA [auth X] Interactions & Density Focus chain EA [auth H] Focus chain IA [auth K] Focus chain UA [auth X]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth K] SDF format, chain QA [auth V] SDF format, chain WA [auth Y] MOL2 format, chain JA [auth K] MOL2 format, chain QA [auth V] MOL2 format, chain WA [auth Y] mmCIF format, chain JA [auth K] mmCIF format, chain QA [auth V] mmCIF format, chain WA [auth Y]	JA [auth K], QA [auth V], WA [auth Y]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain JA [auth K] Focus chain QA [auth V] Focus chain WA [auth Y] Interactions & Density Focus chain JA [auth K] Focus chain QA [auth V] Focus chain WA [auth Y]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain MA [auth N] SDF format, chain NA [auth N] SDF format, chain OA [auth U] SDF format, chain ZA [auth b] MOL2 format, chain DA [auth G] MOL2 format, chain MA [auth N] MOL2 format, chain NA [auth N] MOL2 format, chain OA [auth U] MOL2 format, chain ZA [auth b] mmCIF format, chain DA [auth G] mmCIF format, chain MA [auth N] mmCIF format, chain NA [auth N] mmCIF format, chain OA [auth U] mmCIF format, chain ZA [auth b]	DA [auth G], MA [auth N], NA [auth N], OA [auth U], ZA [auth b]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth G] Focus chain MA [auth N] Focus chain NA [auth N] Focus chain OA [auth U] Focus chain ZA [auth b] Interactions & Density Focus chain DA [auth G] Focus chain MA [auth N] Focus chain NA [auth N] Focus chain OA [auth U] Focus chain ZA [auth b]
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 X] SDF format, chain VA [auth Y] SDF format, chain YA [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 X] MOL2 format, chain VA [auth Y] MOL2 format, chain YA [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 X] mmCIF format, chain VA [auth Y] mmCIF format, chain YA [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 X], VA [auth Y], YA [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 X] Focus chain VA [auth Y] Focus chain YA [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 X] Focus chain VA [auth Y] Focus chain YA [auth Z]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.232
R-Value Work: 0.190
R-Value Observed: 0.193
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.52	α = 90
b = 299.48	β = 112.9
c = 145	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	GR 1861/10-3

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release
Version 2.0: 2024-07-17
Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2024-10-23
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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9FT0

Yeast 20S proteasome in complex with epoxyketone inhibitor 42

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Sequence Annotations

Entity ID: 3

UniProt

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

UniProt

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Entity ID: 8

UniProt

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Sequence Annotations

Entity ID: 9

UniProt

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Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Entity ID: 12

UniProt

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Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)