› 6wvb

X-ray diffraction
2.87Å resolution

Takifugu rubripes VKOR-like with warfarin

Released:
DOI: 10.2210/pdb6wvb/pdb
PDB entry 6wvb coloured by chain, front view.
PDB entry 6wvb coloured by chain, side view.
PDB entry 6wvb coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation.
Liu S, Li S, Shen G, Sukumar N, Krezel AM, Li W
Science 371 (2021)
PMID: 33154105

Function and Biology Details

Reaction catalysed: 
Phylloquinol + a protein with a disulfide bond = phylloquinone + a protein with reduced L-cysteine residues
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154521 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Green fluorescent protein; Vitamin K epoxide reductase complex subunit 1-like protein 1 Chain: A
Molecule details ›
Chain: A
Length: 414 amino acids
Theoretical weight: 46.78 KDa
Source organisms: Expression system: Komagataella pastoris
UniProt:
  • Canonical: P42212 (Residues: 1-145, 146-238; Coverage: 100%)
  • Canonical: Q6TEK8 (Residues: 7-175; Coverage: 97%)
Gene names: GFP, vkorc1l1
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand SWF 1 x SWF
1 modified residue:
Ligand CRO 1 x CRO

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: I222
Unit cell:
a: 65.503Å b: 93.386Å c: 162.973Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.241 0.286
Expression system: Komagataella pastoris

Quick links

Citations

2 review citations

The Effects of Warfarin and Direct Oral Anticoagulants on Systemic Vascular Calcification: A Review.
Elango et al. (2021)
1 more

1 mention without citation

Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation.
Liu et al. (2021)