› 5um3

X-ray diffraction
1.2Å resolution

Crystal structure of the V122L mutant of human UBR-box domain from UBR2

Released:
DOI: 10.2210/pdb5um3/pdb
PDB entry 5um3 coloured by chain, front view.
PDB entry 5um3 coloured by chain, side view.
PDB entry 5um3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase.
Muñoz-Escobar J, Matta-Camacho E, Cho C, Kozlov G, Gehring K
Structure 25 719-729.e3 (2017)
PMID: 28392261

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184900 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase UBR2 Chain: A
Molecule details ›
Chain: A
Length: 75 amino acids
Theoretical weight: 8.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8IWV8 (Residues: 98-167; Coverage: 4%)
Gene names: C6orf133, KIAA0349, UBR2
Sequence domains: Putative zinc finger in N-recognin (UBR box)

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P212121
Unit cell:
a: 29.177Å b: 29.375Å c: 66.052Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.139 0.137 0.158
Expression system: Escherichia coli BL21

Quick links

Citations

3 review citations

E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones.
Ishida et al. (2021)
2 more