3D8Y Hydrolase date May 26, 2008
title Rnase A- 5'-Deoxy-5'-N-Piperidinothymidine Complex
authors D.D.Leonidas, S.E.Zographos, N.G.Oikonomakos
compound source
Molecule: Ribonuclease Pancreatic
Chain: A, B
Synonym: Ribonuclease A, Rnase 1, Rnase A
Ec: 3.1.27.5
 Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Pancreas
symmetry Space Group: C 1 2 1
R_factor 0.189 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.161 32.421 72.567 90.00 90.90 90.00
method X-Ray Diffractionresolution 1.72 Å
ligand FLC, T3S BindingDB enzyme Hydrolase E.C.3.1.27.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • ribonuclease A activity


    • Primary referenceMorpholino, Piperidino, and Pyrrolidino Derivatives of Pyrimidine Nucleosides as Inhibitors of Ribonuclease A: Synthesis, Biochemical, and Crystallographic Evaluation (#) (,) (dagger)., Samanta A, Leonidas DD, Dasgupta S, Pathak T, Zographos SE, Oikonomakos NG, J Med Chem. 2009 Jan 27. PMID:19173562
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (3d8y.pdb1.gz) 23 Kb
  • Biological Unit Coordinates (3d8y.pdb2.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 3D8Y
  • CSU: Contacts of Structural Units for 3D8Y
  • Likely Quarternary Molecular Structure file(s) for 3D8Y
  • Structure Factors (381 Kb)
  • Retrieve 3D8Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D8Y from S2C, [Save to disk]
  • Re-refined 3d8y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3D8Y 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 3D8Y
  • 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 3D8Y, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d8y] [3d8y_B] [3d8y_A]
  • SWISS-PROT database: [P61823]
  • Domain organization of [RNAS1_BOVIN] by SWISSPFAM
  • Domain found in 3D8Y: [RNAse_Pc ] by SMART
    • Other resources with information on 3D8Y
  • Community annotation for 3D8Y at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science