› 2wpk

X-ray diffraction
2.21Å resolution

factor IXa superactive triple mutant, ethylene glycol-soaked

Released:
DOI: 10.2210/pdb2wpk/pdb
PDB 2wpk coloured by chain and viewed from the front.
PDB 2wpk coloured by chain and viewed from the side.
PDB 2wpk coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Structural basis of the cofactor- and substrate-assisted activation of human coagulation factor IXa.
Zögg T, Brandstetter H
Structure 17 1669-78 (2009)
PMID: 20004170

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
Non-polymer only trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Coagulation factor IXa light chain Chain: E
Molecule details ›
Chain: E
Length: 59 amino acids
Theoretical weight: 6.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00740 (Residues: 133-191; Coverage: 14%)
Gene name: F9
Sequence domains: Coagulation Factor Xa inhibitory site
Structure domains: Laminin
D-PHE-PRO-ARG-CHLOROMETHYL KETONE Chain: L
Molecule details ›
Chain: L
Length: 3 amino acids
Theoretical weight: 419 Da
Source organism: synthetic construct
Expression system: Not provided
Coagulation factor IXa heavy chain Chain: S
Molecule details ›
Chain: S
Length: 235 amino acids
Theoretical weight: 26.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00740 (Residues: 227-461; Coverage: 54%)
Gene name: F9
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

2 bound ligands:
Ligand CA 1 x CA
Ligand EDO 1 x EDO
1 modified residue:
Ligand DPN 1 x DPN

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER AXS MICROSTAR
Spacegroup: P212121
Unit cell:
a: 44.07Å b: 66.53Å c: 96.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.206 0.259
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

21 citation in other articles

An interactive mutation database for human coagulation factor IX provides novel insights into the phenotypes and genetics of hemophilia B.
Rallapalli et al. (2013)
20 more

2 mentions without citation

Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity.
Sorensen et al. (2016)
1 more