7VO6 | pdb_00007vo6

High resolution crystal structure of human PSMD10 (Gankyrin)

PDB DOI: https://doi.org/10.2210/pdb7VO6/pdb

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

Deposited: 2021-10-12 Released: 2022-05-11
Deposition Author(s): Mukund Sudharsan, M.G., Venkatraman, P.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.231 (Depositor), 0.187 (DCC)
R-Value Work:
0.196 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A crystal form of PSMD10 Gankyrin with channels accessible to small molecules.

Sudharsan, M.G.M., Venkatraman, P.

(2022) Curr Sci 122: 674-681

DOI: https://doi.org/10.18520/cs/v122/i6/674-681

Macromolecule Content

Total Structure Weight: 24.56 kDa
Atom Count: 1,907
Modeled Residue Count: 224
Deposited Residue Count: 226
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 10	A	226	Homo sapiens	Mutation(s): 0 Gene Names: PSMD10
UniProt & NIH Common Fund Data Resources
Find proteins for O75832 (Homo sapiens) Explore O75832 Go to UniProtKB: O75832
PHAROS: O75832 GTEx: ENSG00000101843
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75832
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLA (Subject of Investigation/LOI) Query on MLA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.231 (Depositor), 0.187 (DCC)
R-Value Work: 0.196 (Depositor)
R-Value Observed: 0.198 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.085	α = 90
b = 60.085	β = 90
c = 122.377	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-11

Deposition Author(s):

Mukund Sudharsan, M.G.

Venkatraman, P.

Funding Organization	Location	Grant Number
Other government	India	ICMR No. 5/13/62/2020-NCD-III

Revision History (Full details and data files)

Version 1.0: 2022-05-11
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.