5ZCO Oxidoreductase date Feb 19, 2018
title Azide-Bound Cytochrome C Oxidase Structure Determined Using Crystals Exposed To 2 Mm Azide Solution For 2 Days
authors A.Shimada, K.Hatano, H.Tadehara, 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 Polypeptide Iv,Cytochrome C O Subunit Iv Isoform 1,Cox 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 Subunit 6, Cytochrome C Oxida Polypeptide Via,Cytochrome C Oxidase 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 Subunit 7, Cytochrome C Oxida Polypeptide Via-Heart,Coxviah,Cytochrome C Oxidase Polypept
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 6b1
Chain: H, U
Synonym: Cytochrome C Oxidase Subunit 8, Cytochrome C Oxida Polypeptide Vii,Cytochrome C Oxidase Subunit Aed,Cytochrome Subunit Vib Isoform 1,Cox Vib-1;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 6c
Chain: I, V
Synonym: Cytochrome C Oxidase Subunit 9, Cytochrome C Oxida Polypeptide Vic,Cytochrome C Oxidase 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 10, Cytochrome C Oxid Subunit Viiic,Viiic,Cytochrome C Oxidase Subunit Viia-Heart Cytochrome C Oxidase Subunit Viia-H,Cytochrome C Oxidase Su Viia-Muscle,Cytochrome C Oxidase Subunit 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 Subunit 11, Cytochrome C Oxid 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 Subunit 12, Cytochrome C Oxid Polypeptide Viiia,Cytochrome C Oxidase 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 Subunit 13, Cytochrome C Oxid Polypeptide Viii-Heart,Cytochrome C Oxidase Subunit 8-1,Cyt Oxidase Subunit 8h,Ix,Viiib
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: P 21 21 21
R_factor 0.164 R_Free 0.189
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.379 206.655 177.589 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand AZI, CDL, CHD, CU, CUA, DMU, EDO, FME, HEA, MG, NA, PEK, PGV, PSC, SAC, TGL, TPO, UNX, 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 referenceX-ray structural analyses of azide-bound cytochrome c oxidases reveal that the H-pathway is critically important for the proton-pumping activity., Shimada A, Hatano K, Tadehara H, Yano N, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S, J Biol Chem. 2018 Aug 3. pii: RA118.003123. doi: 10.1074/jbc.RA118.003123. PMID:30077971
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1382 Kb) [Save to disk]
  • Biological Unit Coordinates (5zco.pdb1.gz) 679 Kb
  • Biological Unit Coordinates (5zco.pdb2.gz) 684 Kb
  • LPC: Ligand-Protein Contacts for 5ZCO
  • CSU: Contacts of Structural Units for 5ZCO
  • Structure Factors (8545 Kb)
  • Retrieve 5ZCO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ZCO from S2C, [Save to disk]
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    • Visual 3D analysis of 5ZCO
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5zco_X] [5zco_B] [5zco_D] [5zco_Q] [5zco_T] [5zco_Z] [5zco_F] [5zco_E] [5zco_W] [5zco_N] [5zco_O] [5zco_P] [5zco_U] [5zco_I] [5zco_K] [5zco_R] [5zco_J] [5zco_M] [5zco_Y] [5zco_G] [5zco_V] [5zco_C] [5zco_H] [5zco_S] [5zco_A] [5zco_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5ZCO
  • Community annotation for 5ZCO at PDBWiki (http://pdbwiki.org)

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