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Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution

Electron Microscopy
4.1Å resolution
PDB entry 7tpp coloured by chain, front view.
PDB entry 7tpp coloured by chain, side view.
PDB entry 7tpp coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero pentamer (preferred)
Entry contents: 5 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Coagulation factor Xa complex
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Multimeric state: hetero pentamer
Accessible surface area: 111491.22 Å2
Buried surface area: 13494.26 Å2
Dissociation area: 4,072.13 Å2
Dissociation energy (ΔGdiss): -13.31 kcal/mol
Dissociation entropy (TΔSdiss): 43.61 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-271972

Macromolecules

Prothrombin
Chain: E
Length: 579 amino acids
Theoretical weight: 65.37 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00734 (Residues: 44-622; Coverage: 97%)
Gene name: F2
Pfam:
InterPro:
Prothrombin in PDB entry 7tpp, assembly 1, front view.
Prothrombin in PDB entry 7tpp, assembly 1, side view.
Prothrombin in PDB entry 7tpp, assembly 1, top view.
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Factor X light chain
Chain: A
Length: 139 amino acids
Theoretical weight: 15.74 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00742 (Residues: 41-179; Coverage: 30%)
Gene name: F10
Pfam:
InterPro:
Factor X light chain in PDB entry 7tpp, assembly 1, front view.
Factor X light chain in PDB entry 7tpp, assembly 1, side view.
Factor X light chain in PDB entry 7tpp, assembly 1, top view.
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Coagulation factor V heavy chain
Chain: C
Length: 709 amino acids
Theoretical weight: 81.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P12259 (Residues: 29-737; Coverage: 32%)
Gene name: F5
Pfam: Multicopper oxidase
InterPro:
Coagulation factor Va in PDB entry 7tpp, assembly 1, front view.
Coagulation factor Va in PDB entry 7tpp, assembly 1, side view.
Coagulation factor Va in PDB entry 7tpp, assembly 1, top view.
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Coagulation factor V light chain
Chain: D
Length: 651 amino acids
Theoretical weight: 75.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P12259 (Residues: 1574-2224; Coverage: 30%)
Gene name: F5
Pfam:
InterPro:
Coagulation factor Va in PDB entry 7tpp, assembly 1, front view.
Coagulation factor Va in PDB entry 7tpp, assembly 1, side view.
Coagulation factor Va in PDB entry 7tpp, assembly 1, top view.
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Activated factor Xa heavy chain
Chain: B
Length: 254 amino acids
Theoretical weight: 28.53 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00742 (Residues: 235-488; Coverage: 56%)
Gene name: F10
Pfam: Trypsin
InterPro:
Activated factor Xa heavy chain in PDB entry 7tpp, assembly 1, front view.
Activated factor Xa heavy chain in PDB entry 7tpp, assembly 1, side view.
Activated factor Xa heavy chain in PDB entry 7tpp, assembly 1, top view.
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