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Madanins (MEROPS I53) are cleaved by thrombin and factor Xa

X-ray diffraction
2.595Å resolution
PDB entry 4boh coloured by chain, front view.
PDB entry 4boh coloured by chain, side view.
PDB entry 4boh coloured by chain, top view.
Source organisms:
Assemblies composition:
hetero trimer (preferred)
hetero dimer
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: alpha-thrombin complex and Thrombin inhibitor Madanin domain-containing protein
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Multimeric state: hetero trimer
Accessible surface area: 12992.15 Å2
Buried surface area: 4083.93 Å2
Dissociation area: 508.72 Å2
Dissociation energy (ΔGdiss): -0.53 kcal/mol
Dissociation entropy (TΔSdiss): 5.32 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133131
Assembly 2
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Assembly Name: alpha-thrombin complex
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Multimeric state: hetero dimer
Accessible surface area: 12806.77 Å2
Buried surface area: 3043.08 Å2
Dissociation area: 1,056.31 Å2
Dissociation energy (ΔGdiss): 9.48 kcal/mol
Dissociation entropy (TΔSdiss): 9.72 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133055
Complex Portal ID: CPX-6222

Macromolecules

Thrombin heavy chain
Chains: A, 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 4boh, assembly 1, front view.
Thrombin heavy chain in PDB entry 4boh, assembly 1, side view.
Thrombin heavy chain in PDB entry 4boh, assembly 1, top view.
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Thrombin light chain
Chains: B, 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 4boh, assembly 1, front view.
Thrombin light chain in PDB entry 4boh, assembly 1, side view.
Thrombin light chain in PDB entry 4boh, assembly 1, top view.
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Thrombin inhibitor Madanin domain-containing protein
Chain: M
Length: 60 amino acids
Theoretical weight: 6.78 KDa
Source organism: Haemaphysalis longicornis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86FP9 (Residues: 20-79; Coverage: 100%)
Pfam: Thrombin inhibitor Madanin
InterPro: Thrombin inhibitor Madanin
Thrombin inhibitor Madanin domain-containing protein in PDB entry 4boh, assembly 1, front view.
Thrombin inhibitor Madanin domain-containing protein in PDB entry 4boh, assembly 1, side view.
Thrombin inhibitor Madanin domain-containing protein in PDB entry 4boh, assembly 1, top view.
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