5LBN | pdb_00005lbn

High-resolution crystal structure of the UBC core domain of UBE2E1/UbcH6

PDB DOI: https://doi.org/10.2210/pdb5LBN/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-06-16 Released: 2018-02-14
Deposition Author(s): Anandapadamanaban, M., Moche, M., Sunnerhagen, M.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.183 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.160 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of a TRIM21 - UBE2E1 complex reveals the specificity of E2 and ubiquitin recognition by TRIM E3 RINGs

Anandapadamanaban, M., Moche, M., Sunnerhagen, M.

To be published.

Macromolecule Content

Total Structure Weight: 17.8 kDa
Atom Count: 1,505
Modelled Residue Count: 154
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 E1	A	158	Homo sapiens	Mutation(s): 0 Gene Names: UBE2E1, UBCH6 EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P51965 (Homo sapiens) Explore P51965 Go to UniProtKB: P51965
PHAROS: P51965 GTEx: ENSG00000170142
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51965
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.183 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.160 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.301	α = 90
b = 40.555	β = 90
c = 91.317	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-14

Deposition Author(s):

Anandapadamanaban, M.

Sunnerhagen, M.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2018-02-14
Type: Initial release
Version 1.1: 2024-05-08
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.