› 3d6o

X-ray diffraction
1.58Å resolution

The RNase A- 5'-Deoxy-5'-N-(ethyl isonipecotatyl)uridine complex

Released:
DOI: 10.2210/pdb3d6o/pdb
PDB entry 3d6o coloured by chain, front view.
PDB entry 3d6o coloured by chain, side view.
PDB entry 3d6o coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Morpholino, piperidino, and pyrrolidino derivatives of pyrimidine nucleosides as inhibitors of ribonuclease A: synthesis, biochemical, and crystallographic evaluation.
Samanta A, Leonidas DD, Dasgupta S, Pathak T, Zographos SE, Oikonomakos NG
J Med Chem 52 932-42 (2009)
PMID: 19173562

Function and Biology Details

Reaction catalysed: 
(1a) an (RNA) containing cytidine = an (RNA)-3'-cytidine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-(RNA)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158390 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribonuclease pancreatic Chains: A, B
Molecule details ›
Chains: A, B
Length: 124 amino acids
Theoretical weight: 13.71 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P61823 (Residues: 27-150; Coverage: 100%)
Gene names: RNASE1, RNS1
Sequence domains: Pancreatic ribonuclease
Structure domains: Ribonuclease A-like domain

Ligands and Environments

1 bound ligand:
Ligand U1S 1 x U1S
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX9.6
Spacegroup: C2
Unit cell:
a: 100.384Å b: 32.876Å c: 72.621Å
α: 90° β: 90.4° γ: 90°
R-values:
R R work R free
0.188 0.186 0.227

Quick links

Citations

10 citation in other articles

3'-Oxo-, amino-, thio- and sulfone-acetic acid modified thymidines: effect of increased acidity on ribonuclease A inhibition.
Datta et al. (2013)
9 more

1 mention without citation

Bridging solvent molecules mediate RNase A - Ligand binding.
Ivanov et al. (2019)