› 5edm

X-ray diffraction
2.2Å resolution

Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I )

Released:
DOI: 10.2210/pdb5edm/pdb
PDB entry 5edm coloured by chain, front view.
PDB entry 5edm coloured by chain, side view.
PDB entry 5edm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin.
Pozzi N, Chen Z, Di Cera E
J Biol Chem 291 6071-82 (2016)
PMID: 26763231

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 Chain: A
Molecule details ›
Chain: A
Length: 568 amino acids
Theoretical weight: 64.84 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00734 (Residues: 44-622; Coverage: 95%)
Gene name: F2
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand MG 6 x MG
Ligand NAG 1 x NAG
Ligand SO4 9 x SO4
Ligand GOL 1 x GOL
1 modified residue:
Ligand CGU 10 x CGU

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2221
Unit cell:
a: 109.884Å b: 168.69Å c: 144.315Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.236
Expression system: Mesocricetus auratus

Quick links

Citations

3 review citations

Plasminogen Activator Inhibitor Type-1 as a Regulator of Fibrosis.
Rabieian et al. (2018)
2 more

11 mentions without citation

Structure of Coagulation Factor II: Molecular Mechanism of Thrombin Generation and Development of Next-Generation Anticoagulants.
Chinnaraj et al. (2018)
10 more