5XDQ Oxidoreductase date Mar 29, 2017
title Bovine Heart Cytochrome C Oxidase In The Fully Oxidized Stat 7.3 At 1.77 Angstrom Resolution
authors F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, K.Shinzawa-Itoh, E.Yam S.Yoshikawa, T.Tsukihara
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: Bovine
Organism_taxid: 9913

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

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

Molecule: Cytochrome C Oxidase Subunit 4 Isoform 1, Mitocho
Chain: D, Q
Synonym: Cytochrome C Oxidase Subunit Iv Isform1, Cytochrom Oxidase Polypeptide Iv,Cytochrome C Oxidase Subunit Iv Isof Iv-1;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

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

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

Molecule: Cytochrome C Oxidase Subunit 6a2, Mitochondrial
Chain: G, T
Synonym: Cytochrome C Oxidase Polypeptide Via-Heart,Coxviah Cytochrome C Oxidase Polypeptide Vib;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 6b1
Chain: H, U
Synonym: Cytochrome C Oxidase Polypeptide Vii,Cytochrome C Subunit Aed,Cytochrome C Oxidase Subunit Vib Isoform 1,Cox
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 6c
Chain: I, V
Synonym: Cytochrome C Oxidase Polypeptide Vic,Cytochrome C Subunit Sta;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 7a1, Mitochondrial
Chain: J, W
Synonym: Cytochrome C Oxidase Subunit Viiic,Viiic,Cytochrom Oxidase Subunit Viia-Heart,Cytochrome C Oxidase Subunit Vii Cytochrome C Oxidase Subunit Viia-Muscle,Cytochrome C Oxida Viia-M;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 7b, Mitochondrial
Chain: K, X
Synonym: Cytochrome C Oxidase Polypeptide Viib,Ihq
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

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

Molecule: Cytochrome C Oxidase Subunit 8b, Mitochondrial
Chain: M, Z
Synonym: Cytochrome C Oxidase Polypeptide Viii-Heart,Cytoch Oxidase Subunit 8-1,Cytochrome C Oxidase Subunit 8h,Ix,Viii
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: P 21 21 21
R_factor 0.164 R_Free 0.190
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.307 205.904 177.526 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.77 Å
ligand CDL, CHD, CU, CUA, DMU, EDO, FME, HEA, MG, NA, PEK, PER, PGV, PSC, SAC, TGL, 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


    H, U


    J, W


    K, X


    N, A


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


    • Q, D


    S, F


    T, G


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


    • Y, L


    Z, M


    Primary referenceStructure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent., Luo F, Shinzawa-Itoh K, Hagimoto K, Shimada A, Shimada S, Yamashita E, Yoshikawa S, Tsukihara T, Acta Crystallogr F Struct Biol Commun. 2017 Jul 1;73(Pt 7):416-422. doi:, 10.1107/S2053230X17008834. Epub 2017 Jun 20. PMID:28695851
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1359 Kb) [Save to disk]
  • Biological Unit Coordinates (5xdq.pdb1.gz) 676 Kb
  • Biological Unit Coordinates (5xdq.pdb2.gz) 672 Kb
  • LPC: Ligand-Protein Contacts for 5XDQ
  • CSU: Contacts of Structural Units for 5XDQ
  • Structure Factors (9364 Kb)
  • Retrieve 5XDQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XDQ from S2C, [Save to disk]
  • Re-refined 5xdq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5XDQ 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 5XDQ
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xdq_J] [5xdq_V] [5xdq_N] [5xdq_D] [5xdq_T] [5xdq_X] [5xdq_C] [5xdq_Z] [5xdq_S] [5xdq_Q] [5xdq_E] [5xdq_U] [5xdq_K] [5xdq_F] [5xdq_O] [5xdq_Y] [5xdq_B] [5xdq_P] [5xdq_W] [5xdq_M] [5xdq_A] [5xdq_G] [5xdq_I] [5xdq_H] [5xdq_R] [5xdq_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XDQ
  • Community annotation for 5XDQ at PDBWiki (http://pdbwiki.org)

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