› 2i7d

X-ray diffraction
1.2Å resolution

Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and Mg2+

Released:
DOI: 10.2210/pdb2i7d/pdb
PDB entry 2i7d coloured by chain, front view.
PDB entry 2i7d coloured by chain, side view.
PDB entry 2i7d coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Rinaldo-Matthis A, Wallden K, Nordlund P

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186188 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5'(3')-deoxyribonucleotidase, cytosolic type Chains: A, B
Molecule details ›
Chains: A, B
Length: 193 amino acids
Theoretical weight: 22.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TCD5 (Residues: 3-195; Coverage: 96%)
Gene names: DNT1, NT5C, UMPH2
Sequence domains: 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ALF 2 x ALF
Ligand DUR 2 x DUR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P1
Unit cell:
a: 39.623Å b: 47.153Å c: 62.384Å
α: 68.92° β: 81.69° γ: 74.99°
R-values:
R R work R free
0.167 0.166 0.196
Expression system: Escherichia coli

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