3DJV Hydrolase date Jun 24, 2008
title Bovine Seminal Ribonuclease- Cytidine 3' Phosphate Complex
authors K.Dossi, D.D.Leonidas, S.E.Zographos, N.G.Oikonomakos
compound source
Molecule: Seminal Ribonuclease
Chain: A, B
Synonym: Seminal Rnase, S-Rnase, Ribonuclease Bs-1
Ec: 3.1.27.5
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.355 58.997 81.994 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand C3P BindingDB enzyme Hydrolase E.C.3.1.27.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • ribonuclease A activity


  • Primary referenceMapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors., Dossi K, Tsirkone VG, Hayes JM, Matousek J, Pouckova P, Soucek J, Zadinova M, Zographos SE, Leonidas DD, Eur J Med Chem. 2009 Nov;44(11):4496-508. Epub 2009 Jul 29. PMID:19643512
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (3djv.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 3DJV
  • CSU: Contacts of Structural Units for 3DJV
  • Likely Quarternary Molecular Structure file(s) for 3DJV
  • Structure Factors (525 Kb)
  • Retrieve 3DJV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DJV from S2C, [Save to disk]
  • Re-refined 3djv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DJV in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3DJV
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3DJV, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3djv] [3djv_B] [3djv_A]
  • SWISS-PROT database: [P00669]
  • Domain organization of [RNS_BOVIN] by SWISSPFAM
  • Domain found in 3DJV: [RNAse_Pc ] by SMART
  • Other resources with information on 3DJV
  • Community annotation for 3DJV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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