› 2g8r

X-ray diffraction
1.7Å resolution

The crystal structure of the RNase A- 3-N-piperidine-4-carboxyl-3-deoxy-ara-uridine complex

Released:
DOI: 10.2210/pdb2g8r/pdb
PDB entry 2g8r coloured by chain, front view.
PDB entry 2g8r coloured by chain, side view.
PDB entry 2g8r coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
The binding of 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine to ribonuclease A in the crystal.
Leonidas DD, Maiti TK, Samanta A, Dasgupta S, Pathak T, Zographos SE, Oikonomakos NG
Bioorg Med Chem 14 6055-64 (2006)
PMID: 16730994

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 domain:

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 N3E 2 x N3E
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: C2
Unit cell:
a: 100.174Å b: 32.53Å c: 72.512Å
α: 90° β: 90.46° γ: 90°
R-values:
R R work R free
0.193 0.191 0.23

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Citations

1 review citation

Lipopolysaccharide sensing an important factor in the innate immune response to Gram-negative bacterial infections: benefits and hazards of LPS hypersensitivity.
Freudenberg et al. (2008)
16 other articles