2DYR Oxidoreductase date Sep 16, 2006
title Bovine Heart Cytochrome C Oxidase At The Fully Oxidized Stat
authors K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa
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
Tissue: Heart

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
Tissue: Heart

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
Tissue: Heart

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
Tissue: Heart

Molecule: Cytochrome C Oxidase Polypeptide Va
Chain: E, R
Ec: 1.9.3.1

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Heart

Molecule: Cytochrome C Oxidase Polypeptide Vb
Chain: F, S
Synonym: Vi
Ec: 1.9.3.1

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Heart

Molecule: Cytochrome C Oxidase Polypeptide Via-Heart
Chain: G, T
Synonym: Coxviah, Polypeptide Vib
Ec: 1.9.3.1

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Heart

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
Tissue: Heart

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
Tissue: Heart

Molecule: Cytochrome C Oxidase Polypeptide Viia-Heart
Chain: J, W
Synonym: Cytochrome C Oxidase Subunit Viia-H, Cox Viia-M, V
Ec: 1.9.3.1

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Heart

Molecule: Cytochrome C Oxidase Polypeptide Viib
Chain: K, X
Synonym: Ihq
Ec: 1.9.3.1

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Heart

Molecule: Cytochrome C Oxidase Polypeptide Viic
Chain: L, Y
Synonym: Viiia
Ec: 1.9.3.1

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Heart

Molecule: Cytochrome C Oxidase Polypeptide Viii-Heart
Chain: M, Z
Synonym: Cytochrome C Oxidase Subunit 8-1, Viiib, Ix
Ec: 1.9.3.1

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Heart
symmetry Space Group: P 21 21 21
R_factor 0.202 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
182.590 205.140 178.250 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CDL, CHD, CU, CUA, DMU, 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 referenceStructures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase., Shinzawa-Itoh K, Aoyama H, Muramoto K, Terada H, Kurauchi T, Tadehara Y, Yamasaki A, Sugimura T, Kurono S, Tsujimoto K, Mizushima T, Yamashita E, Tsukihara T, Yoshikawa S, EMBO J. 2007 Mar 21;26(6):1713-25. Epub 2007 Mar 1. PMID:17332748
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (675 Kb) [Save to disk]
  • Biological Unit Coordinates (2dyr.pdb1.gz) 653 Kb
  • LPC: Ligand-Protein Contacts for 2DYR
  • CSU: Contacts of Structural Units for 2DYR
  • Likely Quarternary Molecular Structure file(s) for 2DYR
  • Structure Factors (5471 Kb)
  • Retrieve 2DYR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DYR from S2C, [Save to disk]
  • Re-refined 2dyr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DYR 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 2DYR
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2DYR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dyr_E] [2dyr_W] [2dyr_J] [2dyr_M] [2dyr_D] [2dyr_A] [2dyr_U] [2dyr_T] [2dyr_B] [2dyr_C] [2dyr_Z] [2dyr_Q] [2dyr_R] [2dyr_G] [2dyr_H] [2dyr_I] [2dyr_Y] [2dyr] [2dyr_P] [2dyr_N] [2dyr_L] [2dyr_V] [2dyr_K] [2dyr_F] [2dyr_S] [2dyr_X] [2dyr_O]
  • SWISS-PROT database: [P00396] [P68530] [P00415] [P00423] [P00426] [P00428] [P04038] [P13183] [P00430] [P10175] [P07471] [P00429] [P07470]
  • Belongs to the proton-translocating cytochrome oxidase (cox) superfamily according to TCDB.
  • Domain organization of [COX1_BOVIN] [COX2_BOVIN] [COX3_BOVIN] [COX41_BOVIN] [COX5A_BOVIN] [COX5B_BOVIN] [COX6C_BOVIN] [COX7B_BOVIN] [COX7C_BOVIN] [COX8B_BOVIN] [CX6A2_BOVIN] [CX6B1_BOVIN] [CX7A1_BOVIN] by SWISSPFAM
  • Other resources with information on 2DYR
  • Community annotation for 2DYR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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