› 8qhq

X-ray diffraction
1.78Å resolution

Crystal structure of human DNPH1 bound to hmdUMP

Released:
DOI: 10.2210/pdb8qhq/pdb
PDB entry 8qhq coloured by chain, front view.
PDB entry 8qhq coloured by chain, side view.
PDB entry 8qhq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1.
Rzechorzek NJ, Kunzelmann S, Purkiss AG, Silva Dos Santos M, MacRae JI, Taylor IA, Fugger K, West SC
OpenAccess logo Nat Commun 14 6809 (2023)
PMID: 37884503

Function and Biology Details

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

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, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 147 amino acids
Theoretical weight: 16.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43598 (Residues: 19-162; Coverage: 83%)
Gene names: C6orf108, DNPH1, RCL
Sequence domains: Nucleoside 2-deoxyribosyltransferase

Ligands and Environments

2 bound ligands:
Ligand 5HU 6 x 5HU
Ligand EDO 8 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 56.648Å b: 67.126Å c: 120.117Å
α: 90° β: 99.63° γ: 90°
R-values:
R R work R free
0.207 0.206 0.224
Expression system: Escherichia coli

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