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 Diffraction	resolution	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	Chain Function Process Component A, B ribonuclease A activity
Primary reference	The 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

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 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] 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)

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