› 6ac9

X-ray diffraction
2.07Å resolution

Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP

Released:
DOI: 10.2210/pdb6ac9/pdb
PDB entry 6ac9 coloured by chain, front view.
PDB entry 6ac9 coloured by chain, side view.
PDB entry 6ac9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of human vaccinia-related kinase 1 in complex with AMP-PNP, a non-hydrolyzable ATP analog.
Ngow YS, Rajan S, Ye H, Yoon HS
Protein Sci 28 524-532 (2019)
PMID: 30461091

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-189297 (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: 370 amino acids
Theoretical weight: 41.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q99986 (Residues: 1-364; Coverage: 92%)
Gene name: VRK1
Sequence domains: Protein kinase domain
Structure domains: Transferase(Phosphotransferase) domain 1

Ligands and Environments

6 bound ligands:
Ligand ANP 4 x ANP
Ligand MG 4 x MG
Ligand SO4 7 x SO4
Ligand CL 4 x CL
Ligand PG4 2 x PG4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: P212121
Unit cell:
a: 92.596Å b: 96.846Å c: 192.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.186 0.223
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes.
Martín-Doncel et al. (2019)
1 more

1 mention without citation

Crystal structure of human vaccinia-related kinase 1 in complex with AMP-PNP, a non-hydrolyzable ATP analog.
Ngow et al. (2019)