9EY9 | pdb_00009ey9

Yeast 20S proteasome in complex with a sybactin derivative (PheSyr)

PDB DOI: https://doi.org/10.2210/pdb9EY9/pdb

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

Deposited: 2024-04-09 Released: 2025-02-19
Deposition Author(s): Praeve, L., Kuttenlochner, W., Tabak, W.W.A., Langer, C., Kaiser, M., Groll, M., Bode, H.B.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.193 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Bioengineering of syrbactin megasynthetases for immunoproteasome inhibitor production

Prave, L., Kuttenlochner, W., Tabak, W.W., Langer, C., Kaiser, M., Groll, M., Bode, H.B.

(2024) Chem 10: 3212-3223

DOI: https://doi.org/10.1016/j.chempr.2024.07.013

Macromolecule Content

Total Structure Weight: 733.26 kDa
Atom Count: 49,448
Modeled Residue Count: 6,332
Deposited Residue Count: 6,610
Unique protein chains: 14

Macromolecules

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23639
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Reference Sequence

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23638
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Reference Sequence

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40302
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Reference Sequence

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 endopeptidase complex	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 endopeptidase complex	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38624
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H71 (Subject of Investigation/LOI) Query on A1H71 Download:Ideal Coordinates CCD File SDF format, chain LA [auth Y] SDF format, chain JA [auth V] SDF format, chain GA [auth K] SDF format, chain DA [auth H] MOL2 format, chain LA [auth Y] MOL2 format, chain JA [auth V] MOL2 format, chain GA [auth K] MOL2 format, chain DA [auth H] mmCIF format, chain LA [auth Y] mmCIF format, chain JA [auth V] mmCIF format, chain GA [auth K] mmCIF format, chain DA [auth H]	DA [auth H], GA [auth K], JA [auth V], LA [auth Y]	sybactin derivative C₃₁ H₄₉ N₅ O₇ HOEOOAXICHBHHS-QBMMHFALSA-N		Interactions Focus chain DA [auth H] Focus chain GA [auth K] Focus chain JA [auth V] Focus chain LA [auth Y] Interactions & Density Focus chain DA [auth H] Focus chain GA [auth K] Focus chain JA [auth V] Focus chain LA [auth Y]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain NA [auth Z] SDF format, chain MA [auth Y] SDF format, chain KA [auth V] SDF format, chain IA [auth N] SDF format, chain HA [auth K] SDF format, chain FA [auth I] SDF format, chain EA [auth H] SDF format, chain CA [auth G] MOL2 format, chain NA [auth Z] MOL2 format, chain MA [auth Y] MOL2 format, chain KA [auth V] MOL2 format, chain IA [auth N] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth I] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain NA [auth Z] mmCIF format, chain MA [auth Y] mmCIF format, chain KA [auth V] mmCIF format, chain IA [auth N] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth I] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] EA [auth H] FA [auth I] HA [auth K] IA [auth N] CA [auth G], EA [auth H], FA [auth I], HA [auth K], IA [auth N], KA [auth V], MA [auth Y], NA [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain HA [auth K] Focus chain IA [auth N] Focus chain KA [auth V] Focus chain MA [auth Y] Focus chain NA [auth Z] Interactions & Density Focus chain CA [auth G] Focus chain EA [auth H] Focus chain FA [auth I] Focus chain HA [auth K] Focus chain IA [auth N] Focus chain KA [auth V] Focus chain MA [auth Y] Focus chain NA [auth Z]