› 1dek

X-ray diffraction
2Å resolution

DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP

Released:
DOI: 10.2210/pdb1dek/pdb
PDB entry 1dek coloured by chain, front view.
PDB entry 1dek coloured by chain, side view.
PDB entry 1dek coloured by chain, top view.
Source organism: Escherichia virus T4
Primary publication:
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
Teplyakov A, Sebastiao P, Obmolova G, Perrakis A, Brush GS, Bessman MJ, Wilson KS
EMBO J 15 3487-97 (1996)
PMID: 8670851

Function and Biology Details

Reaction catalysed: 
ATP + a 2'-deoxyribonucleoside phosphate = ADP + a 2'-deoxyribonucleoside diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137901 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxynucleotide monophosphate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 241 amino acids
Theoretical weight: 27.41 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P04531 (Residues: 1-241; Coverage: 100%)
Gene name: 1
Sequence domains: Deoxynucleotide monophosphate kinase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand DGP 2 x DGP
1 modified residue:
Ligand OCS 2 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: C2
Unit cell:
a: 155.2Å b: 58.5Å c: 75.7Å
α: 90° β: 108.1° γ: 90°
R-values:
R R work R free
0.187 0.187 not available
Expression system: Escherichia coli

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Citations

17 citation in other articles

Evolution and classification of P-loop kinases and related proteins.
Leipe et al. (2003)
16 more

5 mentions without citation

Bacteriophage T4 genome.
Miller et al. (2003)
4 more