› 8epk

X-ray diffraction
2.65Å resolution

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

Released:
DOI: 10.2210/pdb8epk/pdb
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
Primary publication:
An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa.
Kolyadko VN, Layzer JM, Perry K, Sullenger BA, Krishnaswamy S
Proc Natl Acad Sci U S A 121 e2401136121 (2024)
PMID: 38985762

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-246582 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Coagulation factor IXa light chain Chains: A, C
Molecule details ›
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
Sequence domains: Coagulation Factor Xa inhibitory site
Coagulation factor IXa heavy chain Chains: B, D
Molecule details ›
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
Sequence domains: Trypsin
RNA (31-MER) Chains: E, F
Molecule details ›
Chains: E, F
Length: 31 nucleotides
Theoretical weight: 10.12 KDa

Ligands and Environments

2 bound ligands:
Ligand CA 2 x CA
Ligand MG 2 x MG
7 modified residues:
Ligand OMG 12 x OMG
Ligand OMU 4 x OMU
Ligand A2M 12 x A2M
Ligand CFZ 12 x CFZ
Ligand UFT 10 x UFT
Ligand OMC 8 x OMC
Ligand ATD 2 x ATD

Experiments and Validation Details

Entry percentile scores
R-values:
R R work R free
0.233 0.231 0.261
Expression system: Mesocricetus auratus

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