3DTU Oxidoreductase date Jul 15, 2008
title Catalytic Core Subunits (I And II) Of Cytochrome C Oxidase F Rhodobacter Sphaeroides Complexed With Deoxycholic Acid
authors L.Qin, D.A.Mills, L.Buhrow, 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
Strain: 37delta4
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
Fragment: Unp Residues 26-281
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
Strain: 37delta4
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 0.184 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
123.243 132.052 167.966 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand CA, CD, CU, DMU, DXC, HEA, HTO, MG, OH, PO4, TRD 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 referenceA conserved steroid binding site in cytochrome C oxidase., Qin L, Mills DA, Buhrow L, Hiser C, Ferguson-Miller S, Biochemistry. 2008 Sep 23;47(38):9931-3. Epub 2008 Aug 30. PMID:18759498
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (288 Kb) [Save to disk]
  • Biological Unit Coordinates (3dtu.pdb1.gz) 140 Kb
  • Biological Unit Coordinates (3dtu.pdb2.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 3DTU
  • CSU: Contacts of Structural Units for 3DTU
  • Likely Quarternary Molecular Structure file(s) for 3DTU
  • Structure Factors (2309 Kb)
  • Retrieve 3DTU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DTU from S2C, [Save to disk]
  • Re-refined 3dtu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DTU 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 3DTU
  • 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 3DTU, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dtu_D] [3dtu_B] [3dtu] [3dtu_A] [3dtu_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 3DTU
  • Community annotation for 3DTU 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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