5YTO Oxidoreductase date Nov 19, 2017
title Crystal Structure Of Human Superoxide Dismutase I (Hsod1) In With A Napthalene-Catechol Linked Compound.
authors B.Padmanabhan, R.Manjula
compound source
Molecule: Superoxide Dismutase [Cu-Zn]
Chain: A, B, C, D, E, F, G, H, I, J
Synonym: Superoxide Dismutase 1,Hsod1
Ec: 1.15.1.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sod1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Petm11
symmetry Space Group: P 63 2 2
R_factor 0.179 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
243.941 243.941 144.775 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand 946, GOL, PS5, ZN enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, E, B, H, C, D, I, G
  • superoxide dismutase activit...
  • protein binding
  • anterograde axonal transport...
  • retrograde axonal transport

  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (261 Kb) [Save to disk]
  • Biological Unit Coordinates (5yto.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (5yto.pdb2.gz) 55 Kb
  • Biological Unit Coordinates (5yto.pdb3.gz) 55 Kb
  • Biological Unit Coordinates (5yto.pdb4.gz) 53 Kb
  • Biological Unit Coordinates (5yto.pdb5.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 5YTO
  • CSU: Contacts of Structural Units for 5YTO
  • Structure Factors (5329 Kb)
  • Retrieve 5YTO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YTO from S2C, [Save to disk]
  • View 5YTO 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 5YTO
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yto_C] [5yto_I] [5yto_F] [5yto_A] [5yto_D] [5yto_E] [5yto_G] [5yto_B] [5yto_J] [5yto_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YTO
  • Community annotation for 5YTO at PDBWiki (http://pdbwiki.org)

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