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2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules

X-ray diffraction
2.1Å resolution
PDB entry 2b5t coloured by chain, front view.
PDB entry 2b5t coloured by chain, side view.
PDB entry 2b5t coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero pentamer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Thrombin light chain and Antithrombin-III
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Multimeric state: hetero pentamer
Accessible surface area: 45305.81 Å2
Buried surface area: 20754.23 Å2
Dissociation area: 907.66 Å2
Dissociation energy (ΔGdiss): 2.36 kcal/mol
Dissociation entropy (TΔSdiss): 14.13 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133148
Assembly 2
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Assembly Name: Thrombin light chain and Antithrombin-III
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Multimeric state: hetero pentamer
Accessible surface area: 43787.68 Å2
Buried surface area: 22272.36 Å2
Dissociation area: 1,444.94 Å2
Dissociation energy (ΔGdiss): 14.17 kcal/mol
Dissociation entropy (TΔSdiss): 14.16 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133148

Macromolecules

Thrombin light chain
Chains: A, C
Length: 49 amino acids
Theoretical weight: 5.64 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
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 2b5t, assembly 1, front view.
Thrombin light chain in PDB entry 2b5t, assembly 1, side view.
Thrombin light chain in PDB entry 2b5t, assembly 1, top view.
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Thrombin heavy chain
Chains: B, D
Length: 259 amino acids
Theoretical weight: 29.76 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
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 2b5t, assembly 1, front view.
Thrombin heavy chain in PDB entry 2b5t, assembly 1, side view.
Thrombin heavy chain in PDB entry 2b5t, assembly 1, top view.
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Antithrombin-III
Chain: I
Length: 432 amino acids
Theoretical weight: 49.09 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P01008 (Residues: 33-464; Coverage: 100%)
Gene names: AT3, PRO0309, SERPINC1
Pfam: Serpin (serine protease inhibitor)
InterPro:
CATH:
SCOP: Serpins
Antithrombin-III in PDB entry 2b5t, assembly 1, front view.
Antithrombin-III in PDB entry 2b5t, assembly 1, side view.
Antithrombin-III in PDB entry 2b5t, assembly 1, top view.
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