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Thrombin in complex with natural product inhibitor Oscillarin

X-ray diffraction
2.04Å resolution
PDB entry 1riw coloured by chain, front view.
PDB entry 1riw coloured by chain, side view.
PDB entry 1riw coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetramer (preferred)
Entry contents: 4 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: alpha-thrombin complex and Hirudin-2
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Multimeric state: hetero tetramer
Accessible surface area: 12805.22 Å2
Buried surface area: 11479.28 Å2
Dissociation area: 623.8 Å2
Dissociation energy (ΔGdiss): -0.24 kcal/mol
Dissociation entropy (TΔSdiss): 7.68 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133058

Macromolecules

Thrombin light chain
Chain: A
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Pfam: Thrombin light chain
InterPro:
SCOP: Eukaryotic proteases
Thrombin light chain in PDB entry 1riw, assembly 1, front view.
Thrombin light chain in PDB entry 1riw, assembly 1, side view.
Thrombin light chain in PDB entry 1riw, assembly 1, top view.
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Thrombin heavy chain
Chain: B
Length: 147 amino acids
Theoretical weight: 17.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-510; Coverage: 25%)
Gene name: F2
Pfam: Trypsin
InterPro:
CATH: Trypsin-like serine proteases
SCOP: Eukaryotic proteases
Thrombin heavy chain in PDB entry 1riw, assembly 1, front view.
Thrombin heavy chain in PDB entry 1riw, assembly 1, side view.
Thrombin heavy chain in PDB entry 1riw, assembly 1, top view.
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Thrombin heavy chain
Chain: C
Length: 105 amino acids
Theoretical weight: 11.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 518-622; Coverage: 18%)
Gene name: F2
Pfam: Trypsin
InterPro:
CATH: Trypsin-like serine proteases
SCOP: Eukaryotic proteases
Thrombin heavy chain in PDB entry 1riw, assembly 1, front view.
Thrombin heavy chain in PDB entry 1riw, assembly 1, side view.
Thrombin heavy chain in PDB entry 1riw, assembly 1, top view.
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Hirudin-2
Chain: D
Length: 11 amino acids
Theoretical weight: 1.49 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P28504 (Residues: 55-65; Coverage: 17%)
Hirudin-2 in PDB entry 1riw, assembly 1, front view.
Hirudin-2 in PDB entry 1riw, assembly 1, side view.
Hirudin-2 in PDB entry 1riw, assembly 1, top view.
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