1DY5 Hydrolase date Jan 27, 2000
title Deamidated Derivative Of Bovine Pancreatic Ribonuclease
authors L.Esposito, L.Vitagliano, F.Sica, A.Zagari, L.Mazzarella
compound source
Molecule: Ribonuclease A
Chain: A, B
Ec: 3.1.27.5
Mutation: Yes
Other_details: Asn 67 Replaced By A Beta-Aspartyl Residue
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Organ: Pancreas
symmetry Space Group: P 1 21 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.314 37.470 44.915 90.00 94.55 90.00
method X-Ray Diffractionresolution 0.87 Å
ligand ACT, IAS, IPA, SO4 enzyme Hydrolase E.C.3.1.27.5 BRENDA
note 1DY5 is a representative structure
related structures by homologous chain: 1KF3
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • ribonuclease A activity


  • Primary referenceThe 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 2000 Mar 31;297(3):713-32. PMID:10731423
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (1dy5.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (1dy5.pdb2.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 1DY5
  • CSU: Contacts of Structural Units for 1DY5
  • Likely Quarternary Molecular Structure file(s) for 1DY5
  • Structure Factors (2557 Kb)
  • Retrieve 1DY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DY5 from S2C, [Save to disk]
  • Re-refined 1dy5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DY5 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 1DY5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1DY5 1DY5A 1DY5B from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1DY5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dy5a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dy5b_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1dy5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dy5] [1dy5_A] [1dy5_B]
  • SWISS-PROT database: [P61823]
  • Domain organization of [RNAS1_BOVIN] by SWISSPFAM
  • Domain found in 1DY5: [RNAse_Pc ] by SMART
  • Other resources with information on 1DY5
  • Community annotation for 1DY5 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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