2IBZ Oxidoreductase date Sep 12, 2006
title Yeast Cytochrome Bc1 Complex With Stigmatellin
authors C.Hunte
compound source
Molecule: Ubiquinol-Cytochrome-C Reductase Complex Core Pro
Chain: A
Synonym: Complex III Subunit 1, Cytochrome B-C1 Complex Sub
Ec: 1.10.2.2
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Ubiquinol-Cytochrome-C Reductase Complex Core Pro
Chain: B
Synonym: Complex III Subunit 2, Cytochrome B-C1 Complex Sub
Ubiquinol: Cytochrome-C Oxidoreductase Subunit II
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Cytochrome B
Chain: C
Synonym: Ubiquinol-Cytochrome-C Reductase Complex Cytochrom Subunit, Complex III Subunit Cytb, Cytochrome B-C1 Complex Cytb;
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Cytochrome C1, Heme Protein, Mitochondrial Precur
Chain: D
Synonym: Ubiquinol- Cytochrome-C Reductase Complex Cytochro Subunit, Complex III Subunit Cyt1, Cytochrome B-C1 Complex Cyt1;
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Ubiquinol-Cytochrome C Reductase Iron-Sulfur Subu Mitochondrial Precursor;
Chain: E
Synonym: Complex III Subunit Rip1, Cytochrome B-C1 Complex Rip1, Rieske Iron-Sulfur Protein, Risp;
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Ubiquinol-Cytochrome C Reductase Complex 17 Kda P
Chain: H
Synonym: Mitochondrial Hinge Protein, Complex III Subunit 6 Cytochrome B-C1 Complex Subunit 6, Ubiquinol-Cytochrome C R Subunit Vi;
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Ubiquinol-Cytochrome C Reductase Complex 14 Kda P
Chain: F
Synonym: Complex III Subunit 7, Cytochrome B-C1 Complex Sub
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Ubiquinol-Cytochrome C Reductase Complex Ubiquino Protein Qp-C;
Chain: G
Synonym: Ubiquinol-Cytochrome C Reductase Complex 11 Kda Pr Complex III Subunit 8, Cytochrome B-C1 Complex Subunit 8;
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Ubiquinol-Cytochrome C Reductase Complex 7.3 Kda
Chain: I
Synonym: Complex III Subunit 9, Cytochrome B-C1 Complex Sub
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Variable Heavy Chain Of Antibody Fragment
Chain: X
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Variable Domain Antibody Heavy Chain
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm83
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pask68

Molecule: Variable Light Chain Of Antibody Fragment
Chain: Y
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Variable Domain Antibody Light Chain
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm83
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pask68
symmetry Space Group: C 1 2 1
R_factor 0.222 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
214.473 163.921 147.276 90.00 117.50 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand FES, HEC, SMA, UQ6 enzyme Oxidoreductase E.C.1.10.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • ubiquinol-cytochrome-c reduc...


    • B


    C


    D


    E


    F


    G


    H


    I


    X


    Primary referenceA Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome bc(1) Complex., Lancaster CR, Hunte C, Kelley J 3rd, Trumpower BL, Ditchfield R, J Mol Biol. 2007 Feb 11;. PMID:17337272
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (370 Kb) [Save to disk]
  • Biological Unit Coordinates (2ibz.pdb1.gz) 355 Kb
  • LPC: Ligand-Protein Contacts for 2IBZ
  • CSU: Contacts of Structural Units for 2IBZ
  • Likely Quarternary Molecular Structure file(s) for 2IBZ
  • Retrieve 2IBZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IBZ from S2C, [Save to disk]
    • View 2IBZ 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 2IBZ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2IBZ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ibz_B] [2ibz_E] [2ibz_C] [2ibz_X] [2ibz_D] [2ibz_I] [2ibz_G] [2ibz_F] [2ibz_A] [2ibz_Y] [2ibz] [2ibz_H]
  • SWISS-PROT database: [P07143] [P00163] [P18531] [P07256] [P07257] [P00127] [P00128] [P08525] [P22289] [P08067]
  • Belongs to the proton-translocating quinol:cytochrome c reductase (qcr) superfamily according to TCDB.
  • Domain organization of [CY1_YEAST] [CYB_YEAST] [HVM60_MOUSE] [QCR1_YEAST] [QCR2_YEAST] [QCR6_YEAST] [QCR7_YEAST] [QCR8_YEAST] [QCR9_YEAST] [UCRI_YEAST] by SWISSPFAM
  • Domain found in 2IBZ: [IGv ] by SMART
    • Other resources with information on 2IBZ
  • Community annotation for 2IBZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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