› 4mwo

X-ray diffraction
1.67Å resolution

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor CPB-T

Released:
DOI: 10.2210/pdb4mwo/pdb
PDB entry 4mwo coloured by chain, front view.
PDB entry 4mwo coloured by chain, side view.
PDB entry 4mwo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Conformationally constrained nucleoside phosphonic acids--potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases.
Šimák O, Pachl P, Fábry M, Buděšínský M, Jandušík T, Hnízda A, Skleničková R, Petrová M, Veverka V, Řezáčová P, Brynda J, Rosenberg I
Org Biomol Chem 12 7971-82 (2014)
PMID: 25178098

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 BL21(DE3)
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

4 bound ligands:
Ligand 2E2 1 x 2E2
Ligand PO4 1 x PO4
Ligand K 2 x K
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P43212
Unit cell:
a: 73.974Å b: 73.974Å c: 105.95Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.163 0.191
Expression system: Escherichia coli BL21(DE3)

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Citations

1 citations in other articles

Synthesis of phosphonate derivatives of 2'-deoxy-2'-fluorotetradialdose d-nucleosides and tetradialdose d-nucleosides.
Lášek et al. (2021)