› 5ukf

X-ray diffraction
2.4Å resolution

Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor

Released:
DOI: 10.2210/pdb5ukf/pdb
PDB entry 5ukf coloured by chain, front view.
PDB entry 5ukf coloured by chain, side view.
PDB entry 5ukf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Couñago RM, Allerston CK, Savitsky P, Azevedo H, Godoi PH, Wells CI, Mascarello A, de Souza Gama FH, Massirer KB, Zuercher WJ, Guimarães CRW, Gileadi O
OpenAccess logo Sci Rep 7 7501 (2017)
PMID: 28790404

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-573099 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine/threonine-protein kinase VRK1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 363 amino acids
Theoretical weight: 41.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q99986 (Residues: 3-364; Coverage: 91%)
Gene name: VRK1
Sequence domains: Protein kinase domain
Structure domains: Transferase(Phosphotransferase) domain 1

Ligands and Environments

4 bound ligands:
Ligand 8E1 4 x 8E1
Ligand PO4 7 x PO4
Ligand CL 7 x CL
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 92.138Å b: 96.051Å c: 192.741Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.214
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease.
Yeung et al. (2020)
1 more

2 mentions without citation

Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Couñago et al. (2017)
1 more