3DJQ Hydrolase date Jun 24, 2008
title Bovine Seminal Ribonuclease- Uridine 5' Diphosphate 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 0.201 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.080 59.206 82.723 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.53 Å
ligand UDP 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] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (3djq.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 3DJQ
  • CSU: Contacts of Structural Units for 3DJQ
  • Likely Quarternary Molecular Structure file(s) for 3DJQ
  • Structure Factors (582 Kb)
  • Retrieve 3DJQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DJQ from S2C, [Save to disk]
  • Re-refined 3djq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DJQ 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 3DJQ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3DJQ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3djq_B] [3djq_A] [3djq]
  • SWISS-PROT database: [P00669]
  • Domain organization of [RNS_BOVIN] by SWISSPFAM
  • Domain found in 3DJQ: [RNAse_Pc ] by SMART
  • Other resources with information on 3DJQ
  • Community annotation for 3DJQ 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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