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Thrombin in Complex with a D-Phe-Pro-p-phenol derivative

X-ray diffraction
1.38Å resolution
PDB entry 6t3m coloured by chain, front view.
PDB entry 6t3m coloured by chain, side view.
PDB entry 6t3m 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 variant-2
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Multimeric state: hetero trimer
Accessible surface area: 12846.28 Å2
Buried surface area: 4204.96 Å2
Dissociation area: 567.8 Å2
Dissociation energy (ΔGdiss): -0.08 kcal/mol
Dissociation entropy (TΔSdiss): 7.42 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133076

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:
Thrombin light chain in PDB entry 6t3m, assembly 1, front view.
Thrombin light chain in PDB entry 6t3m, assembly 1, side view.
Thrombin light chain in PDB entry 6t3m, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P00734  
1365101520253035
 
102030TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
UniProt
P00734
Chains
Domains
Secondary structure
Ligand binding sites
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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:
Thrombin heavy chain in PDB entry 6t3m, assembly 1, front view.
Thrombin heavy chain in PDB entry 6t3m, assembly 1, side view.
Thrombin heavy chain in PDB entry 6t3m, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P00734  
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Hirudin variant-2
Chain: I
Length: 11 amino acids
Theoretical weight: 1.49 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P09945 (Residues: 62-72; Coverage: 17%)
Hirudin variant-2 in PDB entry 6t3m, assembly 1, front view.
Hirudin variant-2 in PDB entry 6t3m, assembly 1, side view.
Hirudin variant-2 in PDB entry 6t3m, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P09945  
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