3HB3 Oxidoreductase date May 04, 2009
title High Resolution Crystal Structure Of Paracoccus Denitrifican Cytochrome C Oxidase
authors J.Koepke, H.Angerer, G.Peng
compound source
Molecule: Cytochrome C Oxidase Subunit 1-Beta
Chain: A
Synonym: Cytochrome C Oxidase Polypeptide I-Beta, Cytochrom Subunit 1-Beta;
Ec: 1.9.3.1
Engineered: Yes
 Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266
Gene: Ctadii
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Cytochrome C Oxidase Subunit 2
Chain: B
Synonym: Cytochrome C Oxidase Polypeptide II, Cytochrome Aa 2, Oxidase Aa(3) Subunit 2;
Ec: 1.9.3.1
Engineered: Yes
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266
Gene: Ctac, Coii, Ctab
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Antibody Fv Fragment
Chain: C
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Antibody Fv Fragment
Chain: D
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.218 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.403 150.473 157.185 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand CA, CU1, HEA, LDA, LMT, MN, PEO enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • cytochrome-c oxidase activit...


    • B


    C


    Primary referenceHigh resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways., Koepke J, Olkhova E, Angerer H, Muller H, Peng G, Michel H, Biochim Biophys Acta. 2009 Jun;1787(6):635-45. Epub 2009 Apr 15. PMID:19374884
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (202 Kb) [Save to disk]
  • Biological Unit Coordinates (3hb3.pdb1.gz) 188 Kb
  • LPC: Ligand-Protein Contacts for 3HB3
  • CSU: Contacts of Structural Units for 3HB3
  • Likely Quarternary Molecular Structure file(s) for 3HB3
  • Structure Factors (1732 Kb)
  • Retrieve 3HB3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HB3 from S2C, [Save to disk]
  • Re-refined 3hb3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3HB3 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 3HB3
  • 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 3HB3, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hb3_A] [3hb3_C] [3hb3_D] [3hb3] [3hb3_B]
  • SWISS-PROT database: [P98002] [P08306]
  • Belongs to the proton-translocating cytochrome oxidase (cox) superfamily according to TCDB.
  • Domain organization of [COX1B_PARDE] [COX2_PARDE] by SWISSPFAM
  • Domain found in 3HB3: [IGv ] by SMART
    • Other resources with information on 3HB3
  • Community annotation for 3HB3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science