5B3S Oxidoreductase date Mar 11, 2016
title Bovine Heart Cytochrome C Oxidase In The Carbon Monoxide-Bou Valence State At 1.68 Angstrom Resolution (50 K)
authors J.Baba, A.Shimada, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Ts
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
symmetry Space Group: P 21 21 21
R_factor 0.136 R_Free 0.174
crystal
cell
length a length b length c angle alpha angle beta angle gamma
181.491 203.303 177.484 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.68 Å
ligand CDL, CHD, CMO, 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


    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1393 Kb) [Save to disk]
  • Biological Unit Coordinates (5b3s.pdb1.gz) 693 Kb
  • Biological Unit Coordinates (5b3s.pdb2.gz) 684 Kb
  • LPC: Ligand-Protein Contacts for 5B3S
  • CSU: Contacts of Structural Units for 5B3S
  • Structure Factors (6112 Kb)
  • Retrieve 5B3S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B3S from S2C, [Save to disk]
  • Re-refined 5b3s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5B3S 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 5B3S
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5b3s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5b3s_V] [5b3s_W] [5b3s_U] [5b3s_G] [5b3s_Y] [5b3s_D] [5b3s_B] [5b3s_J] [5b3s] [5b3s_C] [5b3s_K] [5b3s_S] [5b3s_L] [5b3s_F] [5b3s_H] [5b3s_P] [5b3s_R] [5b3s_X] [5b3s_A] [5b3s_N] [5b3s_Z] [5b3s_O] [5b3s_T] [5b3s_I] [5b3s_E] [5b3s_Q] [5b3s_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5B3S
  • Community annotation for 5B3S at PDBWiki (http://pdbwiki.org)

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