5FQ2 | pdb_00005fq2

Crystal structure of human SUMO E1 UFD domain in complex with Ubc9 in a P422 space group.

PDB DOI: https://doi.org/10.2210/pdb5FQ2/pdb

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

Deposited: 2015-12-04 Released: 2016-11-16
Deposition Author(s): Liu, B., Castano, L., Lois, M., Reverter, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.249 (Depositor), 0.255 (DCC)
R-Value Work:
0.229 (Depositor), 0.237 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5FQ2

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

Literature

Crystal Structure of Human Sumo E1 Ufd Domain in Complex with Ubc9.

Liu, B., Castano, L., Lois, M., Reverter, D.

To be published.

Macromolecule Content

Total Structure Weight: 30.09 kDa
Atom Count: 2,100
Modeled Residue Count: 258
Deposited Residue Count: 266
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUMO-CONJUGATING ENZYME UBC9	A	161	Homo sapiens	Mutation(s): 0 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P63279 (Homo sapiens) Explore P63279 Go to UniProtKB: P63279
PHAROS: P63279 GTEx: ENSG00000103275
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63279
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUMO-ACTIVATING ENZYME SUBUNIT 2	B	105	Homo sapiens	Mutation(s): 0 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT2 (Homo sapiens) Explore Q9UBT2 Go to UniProtKB: Q9UBT2
PHAROS: Q9UBT2 GTEx: ENSG00000126261
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UBT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LDH Query on LDH	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MLZ Query on MLZ	B	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.249 (Depositor), 0.255 (DCC)
R-Value Work: 0.229 (Depositor), 0.237 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.614	α = 90
b = 129.614	β = 90
c = 66.578	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-11-16
Type: Initial release
Version 1.1: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Other, Structure summary

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.