3AGN Hydrolase date Apr 03, 2010
title Crystal Structure Of Ustilago Sphaerogena Ribonuclease U2 Co With Adenosine 3'-Monophosphate
authors S.Noguchi
compound source
Molecule: Ribonuclease U2
Chain: A
Synonym: Rnase U2
Ec: 3.1.27.4
 Organism_scientific: Ustilago Sphaerogena
Organism_common: Smut Fungus
Organism_taxid: 5271
symmetry Space Group: P 1 21 1
R_factor 0.117 R_Free 0.127
crystal
cell
length a length b length c angle alpha angle beta angle gamma
37.880 39.789 35.884 90.00 114.99 90.00
method X-Ray Diffractionresolution 0.96 Å
ligand 3AM, CA enzyme Hydrolase E.C.3.1.27.4 BRENDA
note 3AGN is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity
  • ribonuclease activity
  • ribonuclease U2 activity


    • Primary referenceIsomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate., Noguchi S, Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):843-9. Epub 2010 Jun 19. PMID:20606265
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (3agn.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 3AGN
  • CSU: Contacts of Structural Units for 3AGN
  • Structure Factors (353 Kb)
  • Retrieve 3AGN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AGN from S2C, [Save to disk]
  • Re-refined 3agn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3AGN 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 3AGN
  • 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 3AGN, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3agn_A] [3agn]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3AGN
  • Community annotation for 3AGN 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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