› 6g2n

X-ray diffraction
1.4Å resolution

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

Released:
DOI: 10.2210/pdb6g2n/pdb
PDB entry 6g2n coloured by chain, front view.
PDB entry 6g2n coloured by chain, side view.
PDB entry 6g2n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases
Pachl P, Simak O, Budesinsky M, Brynda J, Rosenberg I, Rezacova P
Eur. J. Org. Chem. (2018)

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: 205 amino acids
Theoretical weight: 23.87 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8TCD5 (Residues: 2-201; Coverage: 100%)
Gene names: DNT1, NT5C, UMPH2
Sequence domains: 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand O84 2 x O84
1 modified residue:
Ligand CME 4 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P1
Unit cell:
a: 38.877Å b: 47.231Å c: 61.795Å
α: 67.86° β: 88.69° γ: 77.37°
R-values:
R R work R free
0.152 0.151 0.192
Expression system: Escherichia coli BL21(DE3)

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