› 1hlt

X-ray diffraction
3Å resolution

THE STRUCTURE OF A NONADECAPEPTIDE OF THE FIFTH EGF DOMAIN OF THROMBOMODULIN COMPLEXED WITH THROMBIN

Released:
DOI: 10.2210/pdb1hlt/pdb
PDB entry 1hlt coloured by chain, front view.
PDB entry 1hlt coloured by chain, side view.
PDB entry 1hlt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of a nonadecapeptide of the fifth EGF domain of thrombomodulin complexed with thrombin.
Mathews II, Padmanabhan KP, Tulinksy A, Sadler JE
Biochemistry 33 13547-52 (1994)
PMID: 7947765

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

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133152 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: J, L
Molecule details ›
Chains: J, L
Length: 27 amino acids
Theoretical weight: 3.19 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00734 (Residues: 334-360; Coverage: 5%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chains: H, K
Molecule details ›
Chains: H, K
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Thrombomodulin Chain: R
Molecule details ›
Chain: R
Length: 19 amino acids
Theoretical weight: 2.15 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P07204 (Residues: 426-444; Coverage: 3%)
Gene names: THBD, THRM
Sequence domains: Complement Clr-like EGF-like

Ligands and Environments

1 bound ligand:
Ligand 0G6 2 x 0G6
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P43
Unit cell:
a: 50.9Å b: 50.9Å c: 325.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.146 0.146 not available
Expression system: Not provided

Quick links

Citations

4 review citations

Thrombin domains: structure, function and interaction with platelet receptors.
De Cristofaro et al. (2003)
3 more

1 mention without citation

Structure-based drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages.
Singh et al. (2020)