3ABM Oxidoreductase date Dec 16, 2009
title Bovine Heart Cytochrome C Oxidase At The Fully Oxidized Stat X-Ray Exposure Dataset)
authors H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, 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: Bovine
Organism_taxid: 9913

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: Bovine
Organism_taxid: 9913

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: Bovine
Organism_taxid: 9913

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: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 5a
Chain: E, R
Synonym: Cytochrome C Oxidase Polypeptide Va
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 5b
Chain: F, S
Synonym: Cytochrome C Oxidase Polypeptide Vb, Cytochrome C Polypeptide Via;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 6a2
Chain: G, T
Synonym: Cytochrome C Oxidase Polypeptide Via-Heart, Coxvia Cytochrome C Oxidase Polypeptide Vib;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 6b1
Chain: H, U
Synonym: Cytochrome C Oxidase Subunit Vib Isoform 1, Cox Vi Cytochrome C Oxidase Polypeptide Vii, Cytochrome C Oxidase Aed;
Ec: 1.9.3.1
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;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Polypeptide 7a1
Chain: J, W
Synonym: Cytochrome C Oxidase Polypeptide Viia-Heart, Cytoc Oxidase Subunit Viia-H, Cox Viia-M, Viiic;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 7b
Chain: K, X
Synonym: Cytochrome C Oxidase Polypeptide Viib, Ihq
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 7c
Chain: L, Y
Synonym: Cytochrome C Oxidase Polypeptide Viic, Cytochrome Polypeptide Viiia;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Cytochrome C Oxidase Subunit 8b
Chain: M, Z
Synonym: Cytochrome C Oxidase Subunit 8h, Cytochrome C Oxid Polypeptide Viii-Heart, Cytochrome C Oxidase Subunit 8-1, V
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: P 21 21 21
R_factor 0.181 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.697 206.991 178.251 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CDL, CHD, CU, CUA, DMU, FME, HEA, MG, NA, PEK, PER, PGV, PSC, 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 referenceA peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump., Aoyama H, Muramoto K, Shinzawa-Itoh K, Hirata K, Yamashita E, Tsukihara T, Ogura T, Yoshikawa S, Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2165-9. Epub 2009 Jan 21. PMID:19164527
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (663 Kb) [Save to disk]
  • Biological Unit Coordinates (3abm.pdb1.gz) 327 Kb
  • Biological Unit Coordinates (3abm.pdb2.gz) 324 Kb
  • LPC: Ligand-Protein Contacts for 3ABM
  • CSU: Contacts of Structural Units for 3ABM
  • Structure Factors (3770 Kb)
  • Retrieve 3ABM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ABM from S2C, [Save to disk]
  • Re-refined 3abm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3ABM 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 3ABM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3ABM, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3abm_P] [3abm_M] [3abm_K] [3abm_R] [3abm_D] [3abm_Z] [3abm_G] [3abm_O] [3abm_E] [3abm_A] [3abm_C] [3abm_X] [3abm_Y] [3abm_J] [3abm_I] [3abm_V] [3abm_T] [3abm_W] [3abm_S] [3abm_B] [3abm_Q] [3abm_U] [3abm_N] [3abm] [3abm_H] [3abm_F] [3abm_L]
  • 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 3ABM
  • Community annotation for 3ABM 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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