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Crystal structures of protease nexin-1 in complex with S195A thrombin

X-ray diffraction
2.8Å resolution
PDB entry 4dy7 coloured by chain, front view.
PDB entry 4dy7 coloured by chain, side view.
PDB entry 4dy7 coloured by chain, top view.
Source organism: Homo sapiens
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 Glia-derived nexin
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Multimeric state: hetero trimer
Accessible surface area: 26311.97 Å2
Buried surface area: 5859.15 Å2
Dissociation area: 783.1 Å2
Dissociation energy (ΔGdiss): 3.45 kcal/mol
Dissociation entropy (TΔSdiss): 12.97 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133071
Assembly 2
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Assembly Name: alpha-thrombin complex and Glia-derived nexin
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Multimeric state: hetero trimer
Accessible surface area: 27545.13 Å2
Buried surface area: 3900.22 Å2
Dissociation area: 1,037.53 Å2
Dissociation energy (ΔGdiss): 0.88 kcal/mol
Dissociation entropy (TΔSdiss): 12.94 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133071

Macromolecules

Thrombin light chain
Chains: A, D
Length: 49 amino acids
Theoretical weight: 5.64 KDa
Source organism: Homo sapiens
Expression system: Cricetinae gen. sp.
UniProt:
  • Canonical: P00734 (Residues: 315-363; Coverage: 8%)
Gene name: F2
Pfam: Thrombin light chain
InterPro:
CATH: Thrombin light chain domain
Thrombin light chain in PDB entry 4dy7, assembly 1, front view.
Thrombin light chain in PDB entry 4dy7, assembly 1, side view.
Thrombin light chain in PDB entry 4dy7, assembly 1, top view.
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Thrombin heavy chain
Chains: B, E
Length: 259 amino acids
Theoretical weight: 29.76 KDa
Source organism: Homo sapiens
Expression system: Cricetinae gen. sp.
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 4dy7, assembly 1, front view.
Thrombin heavy chain in PDB entry 4dy7, assembly 1, side view.
Thrombin heavy chain in PDB entry 4dy7, assembly 1, top view.
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Glia-derived nexin
Chains: C, F
Length: 379 amino acids
Theoretical weight: 41.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P07093 (Residues: 20-398; Coverage: 100%)
Gene names: PI7, PN1, SERPINE2
Pfam: Serpin (serine protease inhibitor)
InterPro:
CATH:
Glia-derived nexin in PDB entry 4dy7, assembly 1, front view.
Glia-derived nexin in PDB entry 4dy7, assembly 1, side view.
Glia-derived nexin in PDB entry 4dy7, assembly 1, top view.
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