1G65

Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity of alpha,beta-epoxyketone proteasome inhibitors

PDB DOI: https://doi.org/10.2210/pdb1G65/pdb

Classification: HYDROLASE/HYDROLASE inhibitor
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): No

Deposited: 2000-11-03 Released: 2000-11-27
Deposition Author(s): Groll, M., Kim, K.B., Kairies, N., Huber, R., Crews, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.336 (Depositor)
R-Value Work:
0.283 (Depositor)
R-Value Observed:
0.286 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Epoxomicin:20S Proteasome reveals a molecular basis for selectivity of alpha,beta-Epoxyketone Proteasome Inhibitors

Groll, M., Kim, K.B., Kairies, N., Crews, C.

(2000) J Am Chem Soc 122: 1237-1238

DOI: https://doi.org/10.1021/ja993588m

Macromolecule Content

Total Structure Weight: 705.53 kDa
Atom Count: 52,508
Modelled Residue Count: 6,378
Deposited Residue Count: 6,378
Unique protein chains: 15

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component Y7	A, O	250	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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 LOADING

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component Y13	B, P	244	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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 LOADING

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE6	C, Q	241	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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 LOADING

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PUP2	D, R	242	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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 LOADING

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE5	E, S	233	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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 LOADING

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component C1	F, T	244	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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 LOADING

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component C7-alpha	G, U	243	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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 LOADING

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PUP1	H, V	222	Saccharomyces cerevisiae S288C	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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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PUP3	I, W	204	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component C11	J, X	198	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE2	K, Y	212	Saccharomyces cerevisiae S288C	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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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component C5	L, Z	222	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE4	AA [auth 1], M	233	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
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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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome component PRE3	BA [auth 2], N	196	Saccharomyces cerevisiae S288C	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 LOADING

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
EPOXOMICIN (peptide inhibitor)	CA [auth 3], DA [auth 4]	5	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth I] SDF format, chain KA [auth I] SDF format, chain LA [auth K] SDF format, chain MA [auth L] SDF format, chain NA [auth N] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth I] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth K] MOL2 format, chain MA [auth L] MOL2 format, chain NA [auth N] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth I] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth K] mmCIF format, chain MA [auth L] mmCIF format, chain NA [auth N]	EA [auth D] FA [auth F] GA [auth F] HA [auth G] IA [auth H] EA [auth D], FA [auth F], GA [auth F], HA [auth G], IA [auth H], JA [auth I], KA [auth I], LA [auth K], MA [auth L], NA [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth G] Focus chain IA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth K] Focus chain MA [auth L] Focus chain NA [auth N]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
IML Query on IML	CA [auth 3], DA [auth 4]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		ILE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.336 (Depositor)
R-Value Work: 0.283 (Depositor)
R-Value Observed: 0.286 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.2	α = 90
b = 300.2	β = 112.98
c = 144.02	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-11-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-11-27
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2024-11-06
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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1G65

Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity of alpha,beta-epoxyketone proteasome inhibitors

Crystal Structure of Epoxomicin:20S Proteasome reveals a molecular basis for selectivity of alpha,beta-Epoxyketone Proteasome Inhibitors

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Entity ID: 15

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Experimental Data

Structure Validation

Deposition Data

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