5vof

X-ray diffraction
2.25Å resolution

DesGla-XaS195A Bound to Aptamer 11F7t and Rivaroxaban

Released:

Function and Biology Details

Reaction catalysed:
Selective cleavage of Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-133215 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Activated factor Xa heavy chain Chain: H
Molecule details ›
Chain: H
Length: 233 amino acids
Theoretical weight: 26.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P00742 (Residues: 235-467; Coverage: 51%)
Gene name: F10
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Factor X light chain Chain: L
Molecule details ›
Chain: L
Length: 51 amino acids
Theoretical weight: 5.46 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P00742 (Residues: 128-178; Coverage: 11%)
Gene name: F10
Sequence domains: Coagulation Factor Xa inhibitory site
Structure domains: Laminin
DNA/RNA (36-MER) Chain: A
Molecule details ›
Chain: A
Length: 36 nucleotides
Theoretical weight: 11.54 KDa

Ligands and Environments

2 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2221
Unit cell:
a: 55.744Å b: 164.275Å c: 124.521Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.22 0.253
Expression system: Homo sapiens