9FT1

Yeast 20S proteasome in complex with epoxyketone inhibitor 13

PDB DOI: https://doi.org/10.2210/pdb9FT1/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: 2.60 Å
R-Value Free: 0.222
R-Value Work: 0.182
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

This is version 2.0 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: 735.37 kDa
Atom Count: 49,970
Modelled Residue Count: 6,332
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
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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
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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, T	288	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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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
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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-2	H, V	231	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for A0A6A5Q449 (Saccharomyces cerevisiae) Explore A0A6A5Q449 Go to UniProtKB: A0A6A5Q449
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6A5Q449
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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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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
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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 A0A6A5Q5W3 (Saccharomyces cerevisiae) Explore A0A6A5Q5W3 Go to UniProtKB: A0A6A5Q5W3
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6A5Q5W3
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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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IFK (Subject of Investigation/LOI) Query on A1IFK Download Ideal Coordinates CCD File SDF format, chain FA [auth H] SDF format, chain JA [auth K] SDF format, chain MA [auth V] SDF format, chain PA [auth Y] MOL2 format, chain FA [auth H] MOL2 format, chain JA [auth K] MOL2 format, chain MA [auth V] MOL2 format, chain PA [auth Y]	FA [auth H], JA [auth K], MA [auth V], PA [auth Y]	tert-butyl 4-[2-[[(2S)-1-[[(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]amino]-1-oxidanylidene-3-phenylmethoxy-propan-2-yl]amino]-2-oxidanylidene-ethyl]piperazine-1-carboxylate C₄₇ H₇₀ N₆ O₁₁ FDFHFRDWGTWFBD-WFEKHOLKSA-N		Interactions Focus chain FA [auth H] Focus chain JA [auth K] Focus chain MA [auth V] Focus chain PA [auth Y]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain HA [auth J] SDF format, chain LA [auth V] SDF format, chain NA [auth X] SDF format, chain RA [auth b] MOL2 format, chain DA [auth H] MOL2 format, chain HA [auth J] MOL2 format, chain LA [auth V] MOL2 format, chain NA [auth X] MOL2 format, chain RA [auth b]	DA [auth H], HA [auth J], LA [auth V], NA [auth X], RA [auth b]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain HA [auth J] Focus chain LA [auth V] Focus chain NA [auth X] Focus chain RA [auth b]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain GA [auth I] SDF format, chain IA [auth K] SDF format, chain KA [auth N] SDF format, chain OA [auth Y] SDF format, chain QA [auth Z] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain IA [auth K] MOL2 format, chain KA [auth N] MOL2 format, chain OA [auth Y] MOL2 format, chain QA [auth Z]	CA [auth G] EA [auth H] GA [auth I] IA [auth K] KA [auth N] CA [auth G], EA [auth H], GA [auth I], IA [auth K], KA [auth N], OA [auth Y], QA [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth K] Focus chain KA [auth N] Focus chain OA [auth Y] Focus chain QA [auth Z]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.222
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136	α = 90
b = 300.67	β = 113.09
c = 144.54	γ = 90

Software Package:

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

Structure Validation

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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

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 R01GM133198.

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Help and Resources

9FT1

Yeast 20S proteasome in complex with epoxyketone inhibitor 13

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

Entity ID: 1

UniProt

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Sequence Annotations

Entity ID: 2

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Entity ID: 12

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Entity ID: 13

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Entity ID: 14

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)