3FYE Oxidoreductase date Jan 22, 2009
title Catalytic Core Subunits (I And II) Of Cytochrome C Oxidase F Rhodobacter Sphaeroides In The Reduced State
authors L.Qin, D.A.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller
compound source
Molecule: Cytochrome C Oxidase Subunit 1
Chain: A, C
Synonym: Cytochrome C Oxidase Polypeptide I, Cytochrome Aa3 1;
Ec: 1.9.3.1
Engineered: Yes
Organism_scientific: Rhodobacter Sphaeroides
Organism_common: Rhodopseudomonas Sphaeroides
Organism_taxid: 1063
Gene: Ctad
Expression_system: Rhodobacter Sphaeroides
Expression_system_taxid: 1063
Expression_system_strain: Deltaideltaiv
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prk415

Molecule: Cytochrome C Oxidase Subunit 2
Chain: B, D
Synonym: Cytochrome C Oxidase Polypeptide II, Cytochrome Aa 2, Oxidase Aa(3) Subunit 2;
Ec: 1.9.3.1
Engineered: Yes

Organism_scientific: Rhodobacter Sphaeroides
Organism_common: Rhodopseudomonas Sphaeroides
Organism_taxid: 1063
Gene: Ctac, Coxii, Ctab
Expression_system: Rhodobacter Sphaeroides
Expression_system_taxid: 1063
Expression_system_strain: Deltaideltaiv
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prk415
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.613 131.472 176.192 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand CA, CD, CU1, DMU, HEA, HTO, MG, TRD, UNX enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • cytochrome-c oxidase activit...


  • D, B
  • cytochrome-c oxidase activit...


  • Primary referenceRedox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake., Qin L, Liu J, Mills DA, Proshlyakov DA, Hiser C, Ferguson-Miller S, Biochemistry. 2009 Jun 16;48(23):5121-30. PMID:19397279
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (282 Kb) [Save to disk]
  • Biological Unit Coordinates (3fye.pdb1.gz) 139 Kb
  • Biological Unit Coordinates (3fye.pdb2.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 3FYE
  • CSU: Contacts of Structural Units for 3FYE
  • Likely Quarternary Molecular Structure file(s) for 3FYE
  • Structure Factors (2413 Kb)
  • Retrieve 3FYE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FYE from S2C, [Save to disk]
  • Re-refined 3fye structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FYE 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 3FYE
  • 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 3FYE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fye_D] [3fye_B] [3fye_A] [3fye] [3fye_C]
  • SWISS-PROT database: [P33517] [Q03736]
  • Belongs to the proton-translocating cytochrome oxidase (cox) superfamily according to TCDB.
  • Domain organization of [COX1_RHOSH] [COX2_RHOSH] by SWISSPFAM
  • Other resources with information on 3FYE
  • Community annotation for 3FYE 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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