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› 8rps

X-ray diffraction
1.75Å resolution

Crystal structure of human DNPH1 mutant- D80N bound to 5hmdUMP

Released:
DOI: 10.2210/pdb8rps/pdb
Model geometry
Fit model/data
PDB entry 8rps coloured by chain, front view.
PDB entry 8rps coloured by chain, side view.
PDB entry 8rps coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80.
Carberry AE, Devi S, Harrison DJ, da Silva RG
Chembiochem 25 e202400047 (2024)
PMID: 38350003

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-129016 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5-hydroxymethyl-dUMP N-hydrolase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 145 amino acids
Theoretical weight: 16.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43598 (Residues: 20-162; Coverage: 82%)
Gene names: C6orf108, DNPH1, RCL
Sequence domains: Nucleoside 2-deoxyribosyltransferase

Ligands and Environments

1 bound ligand:
Ligand 5HU 2 x 5HU
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: C2
Unit cell:
a: 74.879Å b: 56.828Å c: 88.543Å
α: 90° β: 106.45° γ: 90°
R-values:
R R work R free
0.181 0.179 0.204
Expression system: Escherichia coli

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