PDBe 2gd4

X-ray diffraction
3.3Å resolution

Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex

Released:

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Factor X light chain Chains: A, L
Molecule details ›
Chains: A, L
Length: 58 amino acids
Theoretical weight: 6.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00742 (Residues: 125-182; Coverage: 13%)
Gene name: F10
Sequence domains: Coagulation Factor Xa inhibitory site
Structure domains: Laminin
Activated factor Xa heavy chain Chains: B, H
Molecule details ›
Chains: B, H
Length: 241 amino acids
Theoretical weight: 27.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00742 (Residues: 235-475; Coverage: 53%)
Gene name: F10
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Antithrombin-III Chains: C, I
Molecule details ›
Chains: C, I
Length: 443 amino acids
Theoretical weight: 50.16 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P01008 (Residues: 22-464; Coverage: 100%)
Gene names: AT3, PRO0309, SERPINC1
Sequence domains: Serpin (serine protease inhibitor)
Structure domains:

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX14.1
Spacegroup: C2
Unit cell:
a: 220.263Å b: 60.588Å c: 156.174Å
α: 90° β: 113.14° γ: 90°
R-values:
R R work R free
0.247 0.247 0.298
Expression systems:
  • Escherichia coli
  • Not provided