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X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5

X-ray diffraction
1.602Å resolution
PDB entry 3vxf coloured by chain, front view.
PDB entry 3vxf coloured by chain, side view.
PDB entry 3vxf 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: 10250.59 Å2
Buried surface area: 24740.01 Å2
Dissociation area: 6,200.18 Å2
Dissociation energy (ΔGdiss): 1.34 kcal/mol
Dissociation entropy (TΔSdiss): -8.69 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133090

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 3vxf, assembly 1, front view.
Thrombin light chain in PDB entry 3vxf, assembly 1, side view.
Thrombin light chain in PDB entry 3vxf, 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
Thrombin heavy chain in PDB entry 3vxf, assembly 1, front view.
Thrombin heavy chain in PDB entry 3vxf, assembly 1, side view.
Thrombin heavy chain in PDB entry 3vxf, assembly 1, top view.
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Hirudin-2
Chain: J
Length: 17 amino acids
Theoretical weight: 1.78 KDa
Source organism: unidentified
Expression system: Not provided
UniProt:
  • Canonical: P28504 (Residues: 48-64; Coverage: 26%)
Hirudin-2 in PDB entry 3vxf, assembly 1, front view.
Hirudin-2 in PDB entry 3vxf, assembly 1, side view.
Hirudin-2 in PDB entry 3vxf, assembly 1, top view.
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BIVALIRUDIN
Chain: I
Length: 3 amino acids
Theoretical weight: 419 Da
Source organism: unidentified
Expression system: Not provided
BIVALIRUDIN in PDB entry 3vxf, assembly 1, front view.
BIVALIRUDIN in PDB entry 3vxf, assembly 1, side view.
BIVALIRUDIN in PDB entry 3vxf, assembly 1, top view.
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