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), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.210 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.210 (DCC)
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

View Full Validation Report

Ligand Structure Quality Assessment

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

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.