3DC5 Oxidoreductase date Jun 03, 2008
title Crystal Structure Of A Manganese Superoxide Dismutases From Caenorhabditis Elegans
authors C.H.Trinh, T.Hunter, E.E.Stewart, S.E.V.Phillips, G.J.Hunter
compound source
Molecule: Superoxide Dismutase [Mn] 2
Chain: A, C
Ec: 1.15.1.1
Engineered: Yes
Organism_scientific: Caenorhabditis Elegans
Organism_common: Nematode
Organism_taxid: 6239
Gene: Sod-3, C08a9.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ox326a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptrc-99a
symmetry Space Group: P 41 21 2
R_factor 0.189 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.780 81.780 136.031 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand MLI, MN enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referencePurification, crystallization and X-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans., Trinh CH, Hunter T, Stewart EE, Phillips SE, Hunter GJ, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Dec 1;64(Pt, 12):1110-4. Epub 2008 Nov 28. PMID:19052361
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (3dc5.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 3DC5
  • CSU: Contacts of Structural Units for 3DC5
  • Likely Quarternary Molecular Structure file(s) for 3DC5
  • Structure Factors (380 Kb)
  • Retrieve 3DC5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DC5 from S2C, [Save to disk]
  • Re-refined 3dc5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DC5 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 3DC5
  • 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 3DC5, from MSDmotif at EBI
  • Fold representative 3dc5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dc5_C] [3dc5_A] [3dc5]
  • SWISS-PROT database: [P41977]
  • Domain organization of [SODM2_CAEEL] by SWISSPFAM
  • Other resources with information on 3DC5
  • Community annotation for 3DC5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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