› 3kcg

X-ray diffraction
1.7Å resolution

Crystal structure of the antithrombin-factor IXa-pentasaccharide complex

Released:
DOI: 10.2210/pdb3kcg/pdb
PDB entry 3kcg coloured by chain, front view.
PDB entry 3kcg coloured by chain, side view.
PDB entry 3kcg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-A structure of the ternary complex.
Johnson DJ, Langdown J, Huntington JA
Proc Natl Acad Sci U S A 107 645-50 (2010)
PMID: 20080729

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133192 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (6 distinct):
Coagulation factor IXa light chain Chain: L
Molecule details ›
Chain: L
Length: 59 amino acids
Theoretical weight: 6.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00740 (Residues: 130-188; Coverage: 14%)
Gene name: F9
Sequence domains: Coagulation Factor Xa inhibitory site
Structure domains: Laminin
Coagulation factor IXa heavy chain Chain: H
Molecule details ›
Chain: H
Length: 235 amino acids
Theoretical weight: 26.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00740 (Residues: 227-461; Coverage: 54%)
Gene name: F9
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Antithrombin-III Chain: I
Molecule details ›
Chain: I
Length: 432 amino acids
Theoretical weight: 49.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P01008 (Residues: 33-464; Coverage: 100%)
Gene names: AT3, PRO0309, SERPINC1
Sequence domains: Serpin (serine protease inhibitor)
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: Z9L, Z9K, GU6, GU1, Z9H
Carbohydrate polymer
2 bound ligands:
Ligand CA 1 x CA
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 78.78Å b: 88.44Å c: 147.23Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.208 0.23
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Demystifying heparan sulfate-protein interactions.
Xu et al. (2014)
8 more

18 mentions without citation

Inhibitory serpins. New insights into their folding, polymerization, regulation and clearance.
Gettins et al. (2016)
17 more