› 5to3

X-ray diffraction
2.34Å resolution

Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK

Released:
DOI: 10.2210/pdb5to3/pdb
PDB entry 5to3 coloured by chain, front view.
PDB entry 5to3 coloured by chain, side view.
PDB entry 5to3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Rational Design of Protein C Activators.
Barranco-Medina S, Murphy M, Pelc L, Chen Z, Di Cera E, Pozzi N
Sci Rep 7 44596 (2017)
PMID: 28294177

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133053 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: A
Molecule details ›
Chain: A
Length: 46 amino acids
Theoretical weight: 5.37 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00734 (Residues: 318-363; Coverage: 8%)
Gene name: F2
Sequence domains: Thrombin light chain
Structure domains: Thrombin light chain domain
Thrombin heavy chain; Thrombomodulin Chain: B
Molecule details ›
Chain: B
Length: 409 amino acids
Theoretical weight: 44.62 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00734 (Residues: 364-621; Coverage: 43%)
  • Canonical: P07204 (Residues: 363-483; Coverage: 22%)
Gene names: F2, THBD, THRM
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand 0G6 1 x 0G6
Ligand K 1 x K
Ligand NA 1 x NA
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2221
Unit cell:
a: 62.939Å b: 162.174Å c: 128.859Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.255
Expression system: Cricetulus griseus

Quick links

Citations

1 citations in other articles

PC Deficiency Testing: Thrombin-Thrombomodulin as PC Activator and Aptamer-Based Enzyme Capturing Increase Diagnostic Accuracy.
Reda et al. (2021)

1 mention without citation

Rational Design of Protein C Activators.
Barranco-Medina et al. (2017)