› 1nl1

X-ray diffraction
1.9Å resolution

BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION

Released:
DOI: 10.2210/pdb1nl1/pdb
PDB entry 1nl1 coloured by chain, front view.
PDB entry 1nl1 coloured by chain, side view.
PDB entry 1nl1 coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins.
Huang M, Rigby AC, Morelli X, Grant MA, Huang G, Furie B, Seaton B, Furie BC
Nat Struct Biol 10 751-6 (2003)
PMID: 12923575

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:
  • not assigned
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133162 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Activation peptide fragment 1 Chain: A
Molecule details ›
Chain: A
Length: 147 amino acids
Theoretical weight: 16.97 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 44-190; Coverage: 25%)
Gene name: F2
Sequence domains:
Structure domains: Plasminogen Kringle 4

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 1 x NAG
Ligand CA 7 x CA
1 modified residue:
Ligand CGU 10 x CGU

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P212121
Unit cell:
a: 39.188Å b: 53.443Å c: 128.173Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.219 0.253

Quick links

Citations

54 review citations

Membrane recognition by phospholipid-binding domains.
Lemmon MA. (2008)
53 more

4 mentions without citation

Crystal structure of prothrombin reveals conformational flexibility and mechanism of activation.
Pozzi et al. (2013)
3 more