› 4fh1

X-ray diffraction
2.61Å resolution

S. cerevisiae Ubc13-N79A

Released:
DOI: 10.2210/pdb4fh1/pdb
PDB entry 4fh1 coloured by chain, front view.
PDB entry 4fh1 coloured by chain, side view.
PDB entry 4fh1 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
A conserved asparagine has a structural role in ubiquitin-conjugating enzymes.
Berndsen CE, Wiener R, Yu IW, Ringel AE, Wolberger C
Nat Chem Biol 9 154-6 (2013)
PMID: 23292652

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156556 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin-conjugating enzyme E2 13 Chain: A
Molecule details ›
Chain: A
Length: 153 amino acids
Theoretical weight: 17.43 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P52490 (Residues: 1-153; Coverage: 100%)
Gene names: UBC13, YD6652.04, YDR092W
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

1 bound ligand:
Ligand NHE 1 x NHE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P3121
Unit cell:
a: 77.026Å b: 77.026Å c: 68.35Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.219 0.246
Expression system: Escherichia coli

Quick links

Citations

15 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
14 more

1 mention without citation

A conserved asparagine has a structural role in ubiquitin-conjugating enzymes.
Berndsen et al. (2013)