› 3vn4

X-ray diffraction
2.8Å resolution

Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)

Released:
DOI: 10.2210/pdb3vn4/pdb
PDB entry 3vn4 coloured by chain, front view.
PDB entry 3vn4 coloured by chain, side view.
PDB entry 3vn4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure and enzymatic activity of an ADAMTS-13 mutant with the East Asian-specific P475S polymorphism.
Akiyama M, Nakayama D, Takeda S, Kokame K, Takagi J, Miyata T
J Thromb Haemost 11 1399-406 (2013)
PMID: 23621748

Function and Biology Details

Reaction catalysed: 
The enzyme cleaves the von Willebrand factor at bond 842-Tyr-|-Met-843 within the A2 domain
Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-181181 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
A disintegrin and metalloproteinase with thrombospondin motifs 13 Chain: A
Molecule details ›
Chain: A
Length: 410 amino acids
Theoretical weight: 45.34 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: Q76LX8 (Residues: 287-685; Coverage: 29%)
Gene names: ADAMTS13, C9orf8, UNQ6102/PRO20085
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: FUC, BGC
Carbohydrate polymer
2 bound ligands:
Ligand NAG 1 x NAG
Ligand MAN 1 x MAN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: C2
Unit cell:
a: 153.378Å b: 53.243Å c: 76.615Å
α: 90° β: 111.56° γ: 90°
R-values:
R R work R free
0.232 0.229 0.277
Expression system: Cricetulus griseus

Quick links

Citations

4 review citations

ADAMTS-13 and von Willebrand factor: a dynamic duo.
South et al. (2018)
3 more

3 mentions without citation

ADAM and ADAMTS Family Proteins and Snake Venom Metalloproteinases: A Structural Overview.
Takeda S. (2016)
2 more