› 3djx

X-ray diffraction
1.69Å resolution

Bovine Seminal Ribonuclease- cytidine 5' phosphate complex

Released:
DOI: 10.2210/pdb3djx/pdb
PDB entry 3djx coloured by chain, front view.
PDB entry 3djx coloured by chain, side view.
PDB entry 3djx coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors.
Dossi K, Tsirkone VG, Hayes JM, Matousek J, Poucková P, Soucek J, Zadinova M, Zographos SE, Leonidas DD
Eur J Med Chem 44 4496-508 (2009)
PMID: 19643512

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132818 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Seminal ribonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 124 amino acids
Theoretical weight: 13.63 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00669 (Residues: 27-150; Coverage: 100%)
Gene name: SRN
Sequence domains: Pancreatic ribonuclease
Structure domains: Ribonuclease A-like domain

Ligands and Environments

1 bound ligand:
Ligand C5P 2 x C5P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P212121
Unit cell:
a: 48.585Å b: 59.016Å c: 82.247Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.204

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Citations

1 review citation

Nucleotide binding architecture for secreted cytotoxic endoribonucleases.
Boix et al. (2013)
3 other articles