› 4yik

X-ray diffraction
1.48Å resolution

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

Released:
DOI: 10.2210/pdb4yik/pdb
PDB entry 4yik coloured by chain, front view.
PDB entry 4yik coloured by chain, side view.
PDB entry 4yik 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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192472 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5'(3')-deoxyribonucleotidase, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 201 amino acids
Theoretical weight: 23.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NPB1 (Residues: 32-227; Coverage: 86%)
Gene names: DNT2, NT5M
Sequence domains: 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand MG 1 x MG
Ligand GOL 4 x GOL
Ligand 2O2 1 x 2O2
Ligand TRS 1 x TRS
Ligand PEG 5 x PEG
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P43212
Unit cell:
a: 73.87Å b: 73.87Å c: 106.19Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.153 0.176
Expression system: Escherichia coli

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