› 5mql

X-ray diffraction
3.25Å resolution

Crystal structure of dCK mutant C3S in complex with masitinib and UDP

Released:
DOI: 10.2210/pdb5mql/pdb
PDB entry 5mql coloured by chain, front view.
PDB entry 5mql coloured by chain, side view.
PDB entry 5mql coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology.
Hammam K, Saez-Ayala M, Rebuffet E, Gros L, Lopez S, Hajem B, Humbert M, Baudelet E, Audebert S, Betzi S, Lugari A, Combes S, Letard S, Casteran N, Mansfield C, Moussy A, De Sepulveda P, Morelli X, Dubreuil P
Nat Commun 8 1420 (2017)
PMID: 29127277

Function and Biology Details

Reactions catalysed: 
ATP + deoxyguanosine = ADP + dGMP
NTP + deoxycytidine = NDP + dCMP
ATP + deoxyadenosine = ADP + dAMP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151058 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxycytidine kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 289 amino acids
Theoretical weight: 34.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27707 (Residues: 1-260; Coverage: 100%)
Gene name: DCK
Sequence domains: Deoxynucleoside kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

4 bound ligands:
Ligand UDP 4 x UDP
Ligand G65 1 x G65
Ligand DCM 2 x DCM
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P43212
Unit cell:
a: 88.33Å b: 88.33Å c: 342.53Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.215 0.277
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Molecular Mechanisms of TDP-43 Misfolding and Pathology in Amyotrophic Lateral Sclerosis.
Prasad et al. (2019)
4 more

2 mentions without citation

Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology.
Hammam et al. (2017)
1 more