› 1ycp

X-ray diffraction
2.5Å resolution

THE CRYSTAL STRUCTURE OF FIBRINOGEN-AA PEPTIDE 1-23 (F8Y) BOUND TO BOVINE THROMBIN EXPLAINS WHY THE MUTATION OF PHE-8 TO TYROSINE STRONGLY INHIBITS NORMAL CLEAVAGE AT ARGININE-16

Released:
DOI: 10.2210/pdb1ycp/pdb
PDB entry 1ycp coloured by chain, front view.
PDB entry 1ycp coloured by chain, side view.
PDB entry 1ycp coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16.
Malkowski MG, Martin PD, Lord ST, Edwards BF
Biochem J 326 ( Pt 3) 815-22 (1997)
PMID: 9307032

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 domain:

Structure analysis Details

Assemblies composition:
hetero trimer
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133165 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Thrombin light chain Chains: J, L
Molecule details ›
Chains: J, L
Length: 49 amino acids
Theoretical weight: 5.74 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 318-366; Coverage: 8%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.77 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 367-625; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Fibrinopeptide A Chains: F, N
Molecule details ›
Chains: F, N
Length: 23 amino acids
Theoretical weight: 2.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P02671 (Residues: 20-42; Coverage: 3%)
Gene name: FGA
Thrombin heavy chain Chain: K
Molecule details ›
Chain: K
Length: 150 amino acids
Theoretical weight: 17.53 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 367-516; Coverage: 25%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Thrombin heavy chain Chain: M
Molecule details ›
Chain: M
Length: 109 amino acids
Theoretical weight: 12.27 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 517-625; Coverage: 18%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P43212
Unit cell:
a: 88.27Å b: 88.27Å c: 195.53Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.183 0.245
Expression system: Not provided

Quick links

Citations

2 review citations

Molecular recognition mechanisms of thrombin.
Huntington JA. (2005)
1 more

3 mentions without citation

Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.
De et al. (2005)
2 more