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Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A)

X-ray diffraction
2.65Å resolution
PDB entry 8epk coloured by chain, front view.
PDB entry 8epk coloured by chain, side view.
PDB entry 8epk coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 2 distinct polypeptide molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Coagulation factor IXa complex and RNA
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Multimeric state: hetero trimer
Accessible surface area: 16388.37 Å2
Buried surface area: 12550.85 Å2
Dissociation area: 1,761.55 Å2
Dissociation energy (ΔGdiss): 4.76 kcal/mol
Dissociation entropy (TΔSdiss): 22.31 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-246582
Assembly 2
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Assembly Name: Coagulation factor IXa complex and RNA
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Multimeric state: hetero trimer
Accessible surface area: 16295.99 Å2
Buried surface area: 12662.98 Å2
Dissociation area: 1,820.27 Å2
Dissociation energy (ΔGdiss): 6.33 kcal/mol
Dissociation entropy (TΔSdiss): 22.32 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-246582

Macromolecules

Coagulation factor IXa light chain
Chains: A, C
Length: 65 amino acids
Theoretical weight: 7.27 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00740 (Residues: 130-190; Coverage: 14%)
Gene name: F9
Pfam: Coagulation Factor Xa inhibitory site
Coagulation factor IXa light chain in PDB entry 8epk, assembly 1, front view.
Coagulation factor IXa light chain in PDB entry 8epk, assembly 1, side view.
Coagulation factor IXa light chain in PDB entry 8epk, assembly 1, top view.
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Coagulation factor IXa heavy chain
Chains: B, D
Length: 235 amino acids
Theoretical weight: 26.17 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00740 (Residues: 227-461; Coverage: 54%)
Gene name: F9
Pfam: Trypsin
Coagulation factor IXa heavy chain in PDB entry 8epk, assembly 1, front view.
Coagulation factor IXa heavy chain in PDB entry 8epk, assembly 1, side view.
Coagulation factor IXa heavy chain in PDB entry 8epk, assembly 1, top view.
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RNA chains E, F
Name: RNA (31-MER)
Representative chains: E, F
Length: 31 nucleotides
Theoretical weight: 10.12 KDa
RNA (31-MER) in PDB entry 8epk, assembly 1, front view.
RNA (31-MER) in PDB entry 8epk, assembly 1, side view.
RNA (31-MER) in PDB entry 8epk, assembly 1, top view.
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