› 3h8v

X-ray diffraction
2Å resolution

Human Ubiquitin-activating Enzyme 5 in Complex with ATP

Released:
DOI: 10.2210/pdb3h8v/pdb
PDB entry 3h8v coloured by chain, front view.
PDB entry 3h8v coloured by chain, side view.
PDB entry 3h8v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme.
Bacik JP, Walker JR, Ali M, Schimmer AD, Dhe-Paganon S
J Biol Chem 285 20273-80 (2010)
PMID: 20368332

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190465 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin-like modifier-activating enzyme 5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 292 amino acids
Theoretical weight: 32.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9GZZ9 (Residues: 57-329; Coverage: 68%)
Gene names: UBA5, UBE1DC1
Sequence domains: ThiF family
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3221
Unit cell:
a: 77.999Å b: 77.999Å c: 207.005Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.193 0.191 0.224
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism.
Cappadocia et al. (2018)
9 more

8 mentions without citation

Predicting new indications for approved drugs using a proteochemometric method.
Dakshanamurthy et al. (2012)
7 more