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), 0.229 (DCC)
R-Value Work:
0.187 (Depositor), 0.185 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3K9O

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
Modeled Residue Count: 273
Deposited Residue Count: 297
Unique protein chains: 2

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61086
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.229 (DCC)
R-Value Work: 0.187 (Depositor), 0.185 (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

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View more in-depth experimental data

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

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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.