› 4l57

X-ray diffraction
1.08Å resolution

High resolutin structure of human cytosolic 5'(3')-deoxyribonucleotidase

Released:
DOI: 10.2210/pdb4l57/pdb
PDB entry 4l57 coloured by chain, front view.
PDB entry 4l57 coloured by chain, side view.
PDB entry 4l57 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:
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 BL21(DE3)
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 GOL 6 x GOL
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P1
Unit cell:
a: 39.128Å b: 46.493Å c: 61.409Å
α: 68.16° β: 81.47° γ: 75.28°
R-values:
R R work R free
0.144 0.144 0.183
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

1 mention without citation

Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy?
Piergiorge et al. (2017)