3K9O | pdb_00003k9o

The crystal structure of E2-25K and UBB+1 complex

PDB DOI: https://doi.org/10.2210/pdb3K9O/pdb

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

Deposited: 2009-10-16 Released: 2010-09-08
Deposition Author(s): Kang, G.B., Ko, S., Song, S.M., Lee, W., Eom, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.187 (Depositor), 0.180 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural Basis of E2-25K/UBB+1 Interaction for Neurotoxicity of Alzheimer Disease by Proteasome Inhibition

Kang, G.B., Ko, S., Song, S.M., Lee, W., Eom, S.M.

To be published.

Macromolecule Content

Total Structure Weight: 33.31 kDa
Atom Count: 2,326
Modelled Residue Count: 273
Deposited Residue Count: 297
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 K	A	201	Homo sapiens	Mutation(s): 0 Gene Names: UBE2K, HIP2, LIG EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61086 (Homo sapiens) Explore P61086 Go to UniProtKB: P61086
PHAROS: P61086 GTEx: ENSG00000078140
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61086
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	96	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
PHAROS: P0CG48 GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.187 (Depositor), 0.180 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.48	α = 90
b = 50.547	β = 125.01
c = 71.323	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-09-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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.