5XDX Oxidoreductase date Mar 30, 2017
title Bovine Heart Cytochrome C Oxidase In The Reduced State With 1.99 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 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 Polypeptide Via,Cytochrome C Polypeptide Vb,Cytochrome C Oxidase Subunit 6c;
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 Polypeptide Vic
Chain: I, V
Synonym: Cytochrome C Oxidase Subunit Sta,Cytochrome C Oxid Subunit 6c;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit Viia-Heart
Chain: J, W
Synonym: Cytochrome C Oxidase Subunit Viiic,Viiic,Cytochrom Oxidase Subunit Viia-H,Cytochrome C Oxidase Subunit Viia-Mu Cytochrome C Oxidase Subunit Viia-M,Cytochrome C Oxidase Su Mitochondrial;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

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

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

Molecule: Cytochrome C Oxidase Subunit Viii-Heart
Chain: M, Z
Synonym: Cytochrome C Oxidase Subunit 8-1,Cytochrome C Oxid Subunit 8h,Ix,Viiib,Cytochrome C Oxidase Subunit 8b, Mitoch
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: P 21 21 21
R_factor 0.182 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.044 205.691 177.797 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.99 Å
ligand CDL, CHD, CU, CUA, DMU, EDO, FME, HEA, MG, NA, PEK, 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 in the ligand-free reduced state at neutral pH., Luo F, Shinzawa-Itoh K, Hagimoto K, Shimada A, Shimada S, Yamashita E, Yoshikawa S, Tsukihara T, Acta Crystallogr F Struct Biol Commun. 2018 Feb 1;74(Pt 2):92-98. doi:, 10.1107/S2053230X17018532. Epub 2018 Jan 26. PMID:29400318
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1354 Kb) [Save to disk]
  • Biological Unit Coordinates (5xdx.pdb1.gz) 668 Kb
  • Biological Unit Coordinates (5xdx.pdb2.gz) 672 Kb
  • LPC: Ligand-Protein Contacts for 5XDX
  • CSU: Contacts of Structural Units for 5XDX
  • Structure Factors (8117 Kb)
  • Retrieve 5XDX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XDX from S2C, [Save to disk]
    • View 5XDX in 3D
  • Proteopedia, because life has more than 2D.
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    • Visual 3D analysis of 5XDX
  • 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: [5xdx_T] [5xdx_H] [5xdx_P] [5xdx_K] [5xdx_M] [5xdx_U] [5xdx_B] [5xdx_Y] [5xdx_W] [5xdx_E] [5xdx_V] [5xdx_L] [5xdx_D] [5xdx_C] [5xdx_R] [5xdx_G] [5xdx_N] [5xdx_A] [5xdx_Q] [5xdx_S] [5xdx_I] [5xdx_X] [5xdx_F] [5xdx_O] [5xdx_Z] [5xdx_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XDX
  • Community annotation for 5XDX at PDBWiki (http://pdbwiki.org)

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