› 1mkx

X-ray diffraction
2.2Å resolution

THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING

Released:
DOI: 10.2210/pdb1mkx/pdb
PDB entry 1mkx coloured by chain, front view.
PDB entry 1mkx coloured by chain, side view.
PDB entry 1mkx coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding.
Malkowski MG, Martin PD, Guzik JC, Edwards BF
Protein Sci 6 1438-48 (1997)
PMID: 9232645

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 dimer
monomeric
hetero hexamer (preferred)
homo dimer
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-133178 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: 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
Thrombin heavy chain Chain: K
Molecule details ›
Chain: K
Length: 308 amino acids
Theoretical weight: 35.49 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 318-625; Coverage: 51%)
Gene name: F2
Sequence domains:
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: P21212
Unit cell:
a: 87.52Å b: 87.99Å c: 101.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.187 0.255

Quick links

Citations

6 review citations

Thrombin.
Di Cera E. (2008)
5 more

3 mentions without citation

Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick.
Macedo-Ribeiro et al. (2008)
2 more