› 4yih

X-ray diffraction
1.82Å resolution

Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU

Released:
DOI: 10.2210/pdb4yih/pdb
PDB entry 4yih coloured by chain, front view.
PDB entry 4yih coloured by chain, side view.
PDB entry 4yih coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor
Pachl P, Simak O, Rezacova P, Fabry M, Budesinsky M, Rosenberg I, Brynda J
Medchemcomm 6 1635-1638 (2015)

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: 195 amino acids
Theoretical weight: 22.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TCD5 (Residues: 1-195; Coverage: 97%)
Gene names: DNT1, NT5C, UMPH2
Sequence domains: 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand PO4 2 x PO4
Ligand 2O2 2 x 2O2
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P1
Unit cell:
a: 38.818Å b: 46.451Å c: 61.738Å
α: 111.18° β: 88.16° γ: 104.7°
R-values:
R R work R free
0.187 0.185 0.228
Expression system: Escherichia coli

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