4GP4 Structure of Recombinant Cytochrome ba3 Oxidase mutant Y133F from Thermus thermophilus date 2012-08-20
authors Li, Y., Chen, Y., Stout, C.D.
compound source
symmetry
R_factor
R_Free 0.22666
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand CU, CUA, HAS, HEM, OLC, PER enzyme
note 4GP4 supersedes 4F05
Gene
Ontology
ChainFunctionProcessComponent
A
  • cytochrome-c oxidase activit...


    • B
  • cytochrome-c oxidase activit...


    • C


    Primary referenceLigand Access to the Active Site in Thermus thermophilus ba3 and Bovine Heart aa3 Cytochrome Oxidases., McDonald WJ, Funatogawa C, Li Y, Szundi I, Chen Y, Fee JA, Stout CD, Einarsdottir O, Biochemistry. 2013 Jan 2. PMID:23282175
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (4gp4.pdb1.gz) 129 Kb
  • LPC: Ligand-Protein Contacts for 4GP4
  • CSU: Contacts of Structural Units for 4GP4
  • Structure Factors (1059 Kb)
  • Retrieve 4GP4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GP4 from S2C, [Save to disk]
  • Re-refined 4gp4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4GP4 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 4GP4
  • 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 4GP4, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gp4_A] [4gp4_B] [4gp4_C] [4gp4]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4GP4
  • Community annotation for 4GP4 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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