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Thrombin-bound boophilin displays a functional and accessible reactive-site loop

X-ray diffraction
2.35Å resolution
PDB entry 2ody coloured by chain, front view.
PDB entry 2ody coloured by chain, side view.
PDB entry 2ody 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
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Assembly Name: Activation peptide fragment 2 and Boophilin-H2
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Multimeric state: hetero trimer
Accessible surface area: 18581.01 Å2
Buried surface area: 8116.89 Å2
Dissociation area: 1,928.05 Å2
Dissociation energy (ΔGdiss): 6.27 kcal/mol
Dissociation entropy (TΔSdiss): 12.82 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133175
Assembly 2 (preferred)
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Assembly Name: Activation peptide fragment 2 and Boophilin-H2
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Multimeric state: hetero trimer
Accessible surface area: 18983.64 Å2
Buried surface area: 7728.97 Å2
Dissociation area: 1,587.74 Å2
Dissociation energy (ΔGdiss): 15.75 kcal/mol
Dissociation entropy (TΔSdiss): 10.93 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133175

Macromolecules

Thrombin light chain
Chains: A, C
Length: 49 amino acids
Theoretical weight: 5.74 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 318-366; Coverage: 8%)
Gene name: F2
Pfam: Thrombin light chain
InterPro:
CATH: Thrombin light chain domain
Thrombin light chain in PDB entry 2ody, assembly 2, front view.
Thrombin light chain in PDB entry 2ody, assembly 2, side view.
Thrombin light chain in PDB entry 2ody, assembly 2, top view.
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Thrombin heavy chain
Chains: B, D
Length: 259 amino acids
Theoretical weight: 29.77 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00735 (Residues: 367-625; Coverage: 43%)
Gene name: F2
Pfam: Trypsin
InterPro:
CATH: Trypsin-like serine proteases
Thrombin heavy chain in PDB entry 2ody, assembly 2, front view.
Thrombin heavy chain in PDB entry 2ody, assembly 2, side view.
Thrombin heavy chain in PDB entry 2ody, assembly 2, top view.
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Boophilin-H2
Chains: E, F
Length: 127 amino acids
Theoretical weight: 14 KDa
Source organism: Rhipicephalus microplus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8WPI2 (Residues: 16-142; Coverage: 100%)
Pfam: Kunitz/Bovine pancreatic trypsin inhibitor domain
InterPro:
CATH: Pancreatic trypsin inhibitor Kunitz domain
Boophilin-H2 in PDB entry 2ody, assembly 2, front view.
Boophilin-H2 in PDB entry 2ody, assembly 2, side view.
Boophilin-H2 in PDB entry 2ody, assembly 2, top view.
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