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Crystallographic analysis at 3.0-Angstroms resolution of the binding to human thrombin of four active site-directed inhibitors

X-ray diffraction
3Å resolution
PDB entry 1dwe coloured by chain, front view.
PDB entry 1dwe coloured by chain, side view.
PDB entry 1dwe coloured by chain, top view.
Source organisms:
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: alpha-thrombin complex and Hirudin-3A'
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Multimeric state: hetero trimer
Accessible surface area: 13446.77 Å2
Buried surface area: 3270.66 Å2
Dissociation area: 556.28 Å2
Dissociation energy (ΔGdiss): 1.56 kcal/mol
Dissociation entropy (TΔSdiss): 7.77 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133093

Macromolecules

Thrombin light chain
Chain: L
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 1dwe, assembly 1, front view.
Thrombin light chain in PDB entry 1dwe, assembly 1, side view.
Thrombin light chain in PDB entry 1dwe, assembly 1, top view.
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Thrombin heavy chain
Chain: H
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Pfam: Trypsin
InterPro:
CATH: Trypsin-like serine proteases
SCOP: Eukaryotic proteases
Thrombin heavy chain in PDB entry 1dwe, assembly 1, front view.
Thrombin heavy chain in PDB entry 1dwe, assembly 1, side view.
Thrombin heavy chain in PDB entry 1dwe, assembly 1, top view.
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Hirudin-3A'
Chain: I
Length: 11 amino acids
Theoretical weight: 1.41 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P28508 (Residues: 55-65; Coverage: 17%)
Hirudin-3A' in PDB entry 1dwe, assembly 1, front view.
Hirudin-3A' in PDB entry 1dwe, assembly 1, side view.
Hirudin-3A' in PDB entry 1dwe, assembly 1, top view.
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