9P1Q | pdb_00009p1q

Crystal structure of Ube2E3

PDB DOI: https://doi.org/10.2210/pdb9P1Q/pdb

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

Deposited: 2025-06-10 Released: 2026-05-20
Deposition Author(s): Cook, M.W., Brzovic, P.S., Stenkamp, R.E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9P1Q

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

Literature

Crystal structure of Ube2E3

Cook, M.W., Brzovic, P.S., Stenkamp, R.E.

To be published.

Macromolecule Content

Total Structure Weight: 33.11 kDa
Atom Count: 2,608
Modeled Residue Count: 296
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 E3	A, B	148	Homo sapiens	Mutation(s): 0 Gene Names: UBE2E3, UBCE4, UBCH9 EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q969T4 (Homo sapiens) Explore Q969T4 Go to UniProtKB: Q969T4
PHAROS: Q969T4 GTEx: ENSG00000170035
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q969T4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.246 (Depositor), 0.246 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.56	α = 90
b = 62.82	β = 95.46
c = 51.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM098503-01

Revision History (Full details and data files)

Version 1.0: 2026-05-20
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.