3K9S Oxidoreductase date Oct 16, 2009
title Crystal Structure Of The Peroxide-Bound Manganese Superoxide Dismutase.
authors J.C.Porta, A.Vahedi-Faridi, G.E.O.Borgstahl
compound source
Molecule: Superoxide Dismutase [Mn]
Chain: A, B, C, D
Synonym: Mnsod
Engineered: Yes
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12
Gene: B3908, Jw3879, Soda
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ox326a.1
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pttqa10
symmetry Space Group: C 2 2 21
R_factor 0.227 R_Free 0.270
length a length b length c angle alpha angle beta angle gamma
100.849 107.418 180.044 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand MN, PEO enzyme Oxidoreductase E.C. BRENDA
A, D, C, B

Primary referenceStructural Analysis of Peroxide-Soaked MnSOD Crystals Reveals Side-On Binding of Peroxide to Active-Site Manganese., Porta J, Vahedi-Faridi A, Borgstahl GE, J Mol Biol. 2010 Apr 24. PMID:20417642
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (274 Kb) [Save to disk]
  • Biological Unit Coordinates (3k9s.pdb1.gz) 136 Kb
  • Biological Unit Coordinates (3k9s.pdb2.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 3K9S
  • CSU: Contacts of Structural Units for 3K9S
  • Structure Factors (1326 Kb)
  • Retrieve 3K9S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K9S from S2C, [Save to disk]
  • Re-refined 3k9s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K9S 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 3K9S
  • 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 3K9S, from MSDmotif at EBI
  • Fold representative 3k9s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k9s_C] [3k9s_A] [3k9s] [3k9s_D] [3k9s_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3K9S
  • Community annotation for 3K9S 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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