› 7zeh

X-ray diffraction
1.5Å resolution

Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7Guanine

Released:
DOI: 10.2210/pdb7zeh/pdb
PDB entry 7zeh coloured by chain, front view.
PDB entry 7zeh coloured by chain, side view.
PDB entry 7zeh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism.
Kubacka D, Kozarski M, Baranowski MR, Wojcik R, Panecka-Hofman J, Strzelecka D, Basquin J, Jemielity J, Kowalska J
OpenAccess logo Pharmaceuticals (Basel) 15 (2022)
PMID: 35631380

Function and Biology Details

Reactions catalysed: 
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
CMP + H(2)O = cytidine + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188343 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
7-methylguanosine phosphate-specific 5'-nucleotidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 302 amino acids
Theoretical weight: 34.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q969T7 (Residues: 1-300; Coverage: 100%)
Gene names: NT5C3B, NT5C3L
Sequence domains: Pyrimidine 5'-nucleotidase (UMPH-1)

Ligands and Environments

6 bound ligands:
Ligand IPQ 4 x IPQ
Ligand RBL 4 x RBL
Ligand EDO 29 x EDO
Ligand MG 4 x MG
Ligand PO4 4 x PO4
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P1
Unit cell:
a: 60.59Å b: 80.89Å c: 83.17Å
α: 82.219° β: 72.462° γ: 68.202°
R-values:
R R work R free
0.189 0.188 0.22
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

A Novel m7G-Related Genes-Based Signature with Prognostic Value and Predictive Ability to Select Patients Responsive to Personalized Treatment Strategies in Bladder Cancer.
Lai et al. (2022)

1 mention without citation

Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism.
Kubacka et al. (2022)