2Y69 Electron Transport date Jan 20, 2011
title Bovine Heart Cytochrome C Oxidase Re-Refined With Molecular
authors V.R.I.Kaila, E.Oksanen, A.Goldman, M.I.Verkhovsky, D.Sundholm, M.
compound source
Molecule: Cytochrome C Oxidase Subunit 1
Chain: A, N
Synonym: Cytochrome C Oxidase Polypeptide I
Ec: 1.9.3.1
 Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 2
Chain: B, O
Synonym: Cytochrome C Oxidase Polypeptide II
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 3
Chain: C, P
Synonym: Cytochrome C Oxidase Polypeptide III
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 4 Isoform 1
Chain: D, Q
Synonym: Cytochrome C Oxidase Subunit Iv Isoform 1, Cox Iv- Cytochrome C Oxidase Polypeptide Iv;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 5a
Chain: E, R
Synonym: Cytochrome C Oxidase Polypeptide Va
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 5b
Chain: F, S
Synonym: Cytochrome C Oxidase Polypeptide Vb, Cytochrome C Polypeptide Via;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Polypeptide 6a2
Chain: G, T
Synonym: Cytochrome C Oxidase Polypeptide Via-Heart, Coxvia Polypeptide Vib;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit Vib Isoform 1
Chain: H, U
Synonym: Cox Vib-1, Cytochrome C Oxidase Polypeptide Vii, C C Oxidase Subunit Aed;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Polypeptide Vic
Chain: I, V
Synonym: Sta
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Polypeptide 7a1
Chain: J, W
Synonym: Cytochrome C Oxidase Polypeptide Viia-Heart, Cytoc Oxidase Subunit Viia-H, Cox Viia-M, Viiic;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Polypeptide 7b
Chain: K, X
Synonym: Cytochrome C Oxidase Polypeptide Viib, Ihq
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 7c
Chain: L, Y
Synonym: Cytochrome C Oxidase Polypeptide Viic, Cytochrome Polypeptide Viiia;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Polypeptide 8h
Chain: M, Z
Synonym: Cytochrome C Oxidase Polypeptide Viii-Heart, Cytoc Oxidase Subunit 8-1, Viiib, Ix;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.697 206.991 178.251 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CHD, CU, CUA, DMU, HEA, MG, OXY, PEK, PGV, TPO, ZN enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
C, P
  • cytochrome-c oxidase activit...
  • oxidoreduction-driven active...


    • E, R
  • cytochrome-c oxidase activit...


    • H, U


    J, W
  • cytochrome-c oxidase activit...
  • electron transfer activity


    • K, X
  • cytochrome-c oxidase activit...


    • N, A


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


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


    • S, F


    T, G
  • cytochrome-c oxidase activit...
  • enzyme regulator activity


    • V, I
  • cytochrome-c oxidase activit...


    • Y, L
  • cytochrome-c oxidase activit...


    • Z, M
  • cytochrome-c oxidase activit...


    • Primary referenceA combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase., Kaila VR, Oksanen E, Goldman A, Bloch DA, Verkhovsky MI, Sundholm D, Wikstrom M, Biochim Biophys Acta. 2011 Jan 4. PMID:21211513
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (630 Kb) [Save to disk]
  • Biological Unit Coordinates (2y69.pdb1.gz) 311 Kb
  • Biological Unit Coordinates (2y69.pdb2.gz) 312 Kb
  • LPC: Ligand-Protein Contacts for 2Y69
  • CSU: Contacts of Structural Units for 2Y69
  • Structure Factors (6551 Kb)
  • Retrieve 2Y69 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Y69 from S2C, [Save to disk]
  • Re-refined 2y69 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2Y69 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 2Y69
  • 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 2Y69, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2y69_P] [2y69_E] [2y69_Q] [2y69_F] [2y69_C] [2y69_J] [2y69_X] [2y69_B] [2y69_R] [2y69_A] [2y69_G] [2y69_N] [2y69_Z] [2y69_K] [2y69_L] [2y69_H] [2y69_M] [2y69_U] [2y69_D] [2y69_Y] [2y69_W] [2y69_V] [2y69_T] [2y69_S] [2y69_O] [2y69_I] [2y69]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2Y69
  • Community annotation for 2Y69 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