› 1dy5

X-ray diffraction
0.87Å resolution

Deamidated derivative of bovine pancreatic ribonuclease

Released:
DOI: 10.2210/pdb1dy5/pdb
PDB entry 1dy5 coloured by chain, front view.
PDB entry 1dy5 coloured by chain, side view.
PDB entry 1dy5 coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis.
Esposito L, Vitagliano L, Sica F, Sorrentino G, Zagari A, Mazzarella L
J Mol Biol 297 713-32 (2000)
PMID: 10731423

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

3 bound ligands:
Ligand SO4 3 x SO4
Ligand ACT 4 x ACT
Ligand IPA 8 x IPA
1 modified residue:
Ligand IAS 2 x IAS

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: P21
Unit cell:
a: 61.314Å b: 37.47Å c: 44.915Å
α: 90° β: 94.55° γ: 90°
R-values:
R R work R free
0.101 not available 0.12

Quick links

Citations

3 review citations

Protein hydration dynamics in solution: a critical survey.
Halle B. (2004)
2 more

17 mentions without citation

Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions.
Iwaoka et al. (2012)
16 more