› 4l6a

X-ray diffraction
1.4Å resolution

Structure of human mitochondrial 5'(3')-deoxyribonucleotidase

Released:
DOI: 10.2210/pdb4l6a/pdb
PDB entry 4l6a coloured by chain, front view.
PDB entry 4l6a coloured by chain, side view.
PDB entry 4l6a coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors.
Pachl P, Fábry M, Rosenberg I, Simák O, Rezáčová P, Brynda J
Acta Crystallogr D Biol Crystallogr 70 461-70 (2014)
PMID: 24531480

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: 202 amino acids
Theoretical weight: 23.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NPB1 (Residues: 32-228; Coverage: 86%)
Gene names: DNT2, NT5M
Sequence domains: 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand MG 1 x MG
Ligand PO4 1 x PO4
Ligand GOL 9 x GOL
Ligand PEG 4 x PEG
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P43212
Unit cell:
a: 73.41Å b: 73.41Å c: 106.34Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.141 0.141 0.154
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

Conformationally constrained nucleoside phosphonic acids--potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases.
Šimák et al. (2014)
1 more