› 3qdz

X-ray diffraction
2.8Å resolution

Crystal structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR4.

Released:
DOI: 10.2210/pdb3qdz/pdb
PDB entry 3qdz coloured by chain, front view.
PDB entry 3qdz coloured by chain, side view.
PDB entry 3qdz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of thrombin-protease-receptor interactions
Gandhi PS, Chen Z, Appelbaum E, Zapata F, Di Cera E
IUBMB Life 63 375-382 (2011)

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133132 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 31 amino acids
Theoretical weight: 3.65 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00734 (Residues: 333-363; Coverage: 5%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Proteinase-activated receptor 4 Chains: E, F
Molecule details ›
Chains: E, F
Length: 9 amino acids
Theoretical weight: 952 Da
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: Q96RI0 (Residues: 39-47; Coverage: 2%)
Gene names: F2RL3, PAR4

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: C2221
Unit cell:
a: 91.414Å b: 102.876Å c: 146.39Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.304 0.304 0.364
Expression system: Mesocricetus auratus

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