9S2Z | pdb_00009s2z

Crystal structure of Usp10 catalytic domain bound to Ub-PA

PDB DOI: https://doi.org/10.2210/pdb9S2Z/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-23 Released: 2026-11-04
Deposition Author(s): Misra, M., Vollrath, J., Vidov, A., Dikic, I.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.194 (Depositor), 0.198 (DCC)
R-Value Work:
0.169 (Depositor), 0.172 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Mechanistic and structural insights into the ubiquitin specific protease 10

Vollrath, J., Misra, M., Vidov, V., Mato, U.G., Mosler, T., Mukhopadhyay, R., Pahor, N., Stuke, J., Heinz, M., Hartmann, O., van der Heden van Noort, G., Hummer, G., Geurink, P., Diefenbacher, M., Langer, J.D., Dikic, I.

To be published.

Macromolecule Content

Total Structure Weight: 54.18 kDa
Atom Count: 4,156
Modeled Residue Count: 418
Deposited Residue Count: 469
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 10	A	394	Homo sapiens	Mutation(s): 0 Gene Names: USP10, KIAA0190 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q14694 (Homo sapiens) Explore Q14694 Go to UniProtKB: Q14694
PHAROS: Q14694 GTEx: ENSG00000103194
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14694
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B	75	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth B]	Q [auth B], S [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain Q [auth B] Focus chain S [auth B] Interactions & Density Focus chain Q [auth B] Focus chain S [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain E [auth A] MOL2 format, chain O [auth A] MOL2 format, chain E [auth A] mmCIF format, chain O [auth A] mmCIF format, chain E [auth A]	E [auth A], O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain O [auth A] Interactions & Density Focus chain E [auth A] Focus chain O [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] F [auth A] G [auth A] H [auth A] C [auth A], D [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B]
AYE Query on AYE Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	prop-2-en-1-amine C₃ H₇ N VVJKKWFAADXIJK-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]