1YAZ Oxidoreductase date Dec 23, 1998
title Azide-Bound Yeast Cu(II)Zn Superoxide Dismutase Room Temper (298k) Structure
authors P.J.Hart, M.M.Balbirnie, N.L.Ogihara, A.M.Nersissian, M.S.Weiss, J.S.Valentine, D.Eisenberg
compound source
Molecule: Protein (Cuzn Superoxide Dismutase)
Chain: A
Synonym: Yeast Cuzn Sod
Ec: 1.15.1.1
Other_details: Room (298k) Temperature Azide-Bound Structur Copper-Imidazolate Bridge Intact
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Cellular_location: Cytoplasm
symmetry Space Group: H 3 2
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
119.375 119.375 74.543 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å
ligand AZI, CU, ZN enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
related structures by homologous chain: 1PZS, 2JCW
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA structure-based mechanism for copper-zinc superoxide dismutase., Hart PJ, Balbirnie MM, Ogihara NL, Nersissian AM, Weiss MS, Valentine JS, Eisenberg D, Biochemistry 1999 Feb 16;38(7):2167-78. PMID:10026301
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (1yaz.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 1YAZ
  • CSU: Contacts of Structural Units for 1YAZ
  • Likely Quarternary Molecular Structure file(s) for 1YAZ
  • Structure Factors (208 Kb)
  • Retrieve 1YAZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YAZ from S2C, [Save to disk]
  • Re-refined 1yaz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YAZ 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 1YAZ
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YAZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1yaza_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1yaz 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: [1yaz_A] [1yaz]
  • SWISS-PROT database: [P00445]
  • Domain organization of [SODC_YEAST] by SWISSPFAM
  • Other resources with information on 1YAZ
  • Community annotation for 1YAZ 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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