1Q0D Oxidoreductase date Jul 16, 2003
title Crystal Structure Of Ni-Containing Superoxide Dismutase With Ligation Corresponding To The Oxidized State
authors J.Wuerges, J.W.Lee, Y.I.Yim, H.S.Yim, S.O.Kang, K.Djinovic Ca
compound source
Molecule: Superoxide Dismutase [Ni]
Chain: A, B, C, D, E, F, G, H, I, J, K, L
Synonym: Nickel-Containing Superoxide Dismutase; Nisod; Ni- Superoxide Dismutase;
Ec: 1.15.1.1
Other_details: The Asymmetric Unit Contains Two Hexamers
Organism_scientific: Streptomyces Seoulensis
Organism_taxid: 73044
symmetry Space Group: P 21 21 21
R_factor 0.172 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.260 113.749 128.618 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 3NI, SO4 enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
note 1Q0D (Molecule of the Month:pdb94)
related structures by homologous chain: 1Q0F, 1T6I
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, K, E, B, H, C, D, I, G, L


Primary referenceCrystal structure of nickel-containing superoxide dismutase reveals another type of active site., Wuerges J, Lee JW, Yim YI, Yim HS, Kang SO, Carugo KD, Proc Natl Acad Sci U S A 2004 Jun 8;101(23):8569-74. Epub 2004 Jun 1. PMID:15173586
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (255 Kb) [Save to disk]
  • Biological Unit Coordinates (1q0d.pdb1.gz) 126 Kb
  • Biological Unit Coordinates (1q0d.pdb2.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 1Q0D
  • CSU: Contacts of Structural Units for 1Q0D
  • Likely Quarternary Molecular Structure file(s) for 1Q0D
  • Structure Factors (699 Kb)
  • Retrieve 1Q0D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q0D from S2C, [Save to disk]
  • Re-refined 1q0d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Q0D 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 1Q0D
  • 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 1Q0D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q0da_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1q0db_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1q0dc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1q0dd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1q0de_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1q0df_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1q0dg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1q0dh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1q0di_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1q0dj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1q0dk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1q0dl_, region L [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1q0d_J] [1q0d_L] [1q0d_F] [1q0d] [1q0d_K] [1q0d_I] [1q0d_G] [1q0d_A] [1q0d_H] [1q0d_D] [1q0d_E] [1q0d_C] [1q0d_B]
  • SWISS-PROT database: [P80734]
  • Domain organization of [SODN_STRSO] by SWISSPFAM
  • Other resources with information on 1Q0D
  • Community annotation for 1Q0D 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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