5IY5 Oxidoreductase date Mar 24, 2016
title Electron Transfer Complex Of Cytochrome C And Cytochrome C O 2.0 Angstrom Resolution
authors S.Shimada, J.Baba, S.Aoe, A.Shimada, E.Yamashita, 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;
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

Molecule: Cytochrome C
Chain: 1, 2
Organism_scientific: Equus Caballus
Organism_common: Horse
Organism_taxid: 9796
symmetry Space Group: P 1 21 1
R_factor 0.167 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.290 183.872 148.929 90.00 102.12 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ACE, CDL, CHD, CU, CUA, DMU, EDO, FME, HEA, HEC, MG, NA, PEK, PER, PGV, PSC, SAC, TGL, TPO, UNL, ZN enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
2, 1


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


    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1376 Kb) [Save to disk]
  • Biological Unit Coordinates (5iy5.pdb1.gz) 680 Kb
  • Biological Unit Coordinates (5iy5.pdb2.gz) 681 Kb
  • LPC: Ligand-Protein Contacts for 5IY5
  • CSU: Contacts of Structural Units for 5IY5
  • Structure Factors (7410 Kb)
  • Retrieve 5IY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IY5 from S2C, [Save to disk]
  • Re-refined 5iy5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5IY5 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 5IY5
  • 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: [5iy5_D] [5iy5_W] [5iy5_Y] [5iy5_K] [5iy5_1] [5iy5_N] [5iy5_S] [5iy5_A] [5iy5_P] [5iy5] [5iy5_G] [5iy5_R] [5iy5_I] [5iy5_H] [5iy5_U] [5iy5_Q] [5iy5_X] [5iy5_Z] [5iy5_O] [5iy5_T] [5iy5_F] [5iy5_M] [5iy5_C] [5iy5_E] [5iy5_2] [5iy5_V] [5iy5_L] [5iy5_J] [5iy5_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5IY5
  • Community annotation for 5IY5 at PDBWiki (http://pdbwiki.org)

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