› 6c2w

X-ray diffraction
4.12Å resolution

Crystal structure of human prothrombin mutant S101C/A470C

Released:
DOI: 10.2210/pdb6c2w/pdb
PDB entry 6c2w coloured by chain, front view.
PDB entry 6c2w coloured by chain, side view.
PDB entry 6c2w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of prothrombin in the closed form reveals new details on the mechanism of activation.
Chinnaraj M, Chen Z, Pelc LA, Grese Z, Bystranowska D, Di Cera E, Pozzi N
Sci Rep 8 2945 (2018)
PMID: 29440720

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133054 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Prothrombin Chains: A, B
Molecule details ›
Chains: A, B
Length: 582 amino acids
Theoretical weight: 66.31 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00734 (Residues: 44-622; Coverage: 97%)
Gene name: F2
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
2 bound ligands:
Ligand MG 12 x MG
Ligand NAG 2 x NAG
1 modified residue:
Ligand CGU 20 x CGU

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P1
Unit cell:
a: 85.03Å b: 85.074Å c: 153.801Å
α: 105.35° β: 90° γ: 90.05°
R-values:
R R work R free
0.281 0.278 0.333
Expression system: Mesocricetus auratus

Quick links

Citations

3 review citations

Mechanisms of ligand binding.
Di Cera E. (2020)
2 more

7 mentions without citation

Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands.
Troisi et al. (2021)
6 more