› 4p5d

X-ray diffraction
2.11Å resolution

CRYSTAL STRUCTURE OF RAT DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE

Released:
DOI: 10.2210/pdb4p5d/pdb
PDB entry 4p5d coloured by chain, front view.
PDB entry 4p5d coloured by chain, side view.
PDB entry 4p5d coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: synthesis, structural studies and cytotoxic activities.
Amiable C, Paoletti J, Haouz A, Padilla A, Labesse G, Kaminski PA, Pochet S
Eur J Med Chem 85 418-37 (2014)
PMID: 25108359

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128714 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5-hydroxymethyl-dUMP N-hydrolase Chains: A, C
Molecule details ›
Chains: A, C
Length: 152 amino acids
Theoretical weight: 17.17 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O35820 (Residues: 11-151; Coverage: 87%)
Gene names: Dnph1, Rcl
Sequence domains: Nucleoside 2-deoxyribosyltransferase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand N6P 2 x N6P
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P6122
Unit cell:
a: 178.2Å b: 178.2Å c: 56.922Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.175 0.198
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides.
Shaughnessy KH. (2015)
1 more