1PP9 Oxidoreductase date Jun 16, 2003
title Bovine Cytochrome Bc1 Complex With Stigmatellin Bound
authors L.S.Huang, D.Cobessi, E.Y.Tung, E.A.Berry
compound source
Molecule: Ubiquinol-Cytochrome C Reductase Complex Core Pro Mitochondrial;
Chain: A, N
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
 Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Complex Core Pro Mitochondrial;
Chain: B, O
Synonym: Complex III Subunit II
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome B
Chain: C, P
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C1, Heme Protein, Mitochondrial
Chain: D, Q
Synonym: Cytochrome C-1
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Iron-Sulfur Subu Mitochondrial;
Chain: E, R
Synonym: Rieske Iron-Sulfur Protein, Risp, Complex III Subu
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Complex 14 Kda P
Chain: F, S
Synonym: Complex III Subunit Vi
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Complex Ubiquino Protein Qp-C;
Chain: G, T
Synonym: Ubiquinol-Cytochrome C Reductase Complex 9.5 Kda P Complex III Subunit Vii;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Complex 11 Kda P
Chain: H, U
Synonym: Mitochondrial Hinge Protein, Cytochrome C1, Nonhem Protein, Complex III Subunit Viii;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Iron-Sulfur Subu Mitochondrial;
Chain: I, V
Synonym: Rieske Iron-Sulfur Protein, Risp, Complex III Subu
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Complex 7.2 Kda
Chain: J, W
Synonym: Cytochrome C1, Nonheme 7 Kda Protein, Complex III
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
symmetry Space Group: P 21 21 21
R_factor 0.250 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
139.117 171.055 227.204 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand AZI, CDL, FES, GOL, HEC, HEM, JZR, PEE, PO4, SMA, UQ enzyme Oxidoreductase E.C.1.10.2.2 BRENDA
related structures by homologous chain: 1BE3, 1L0L, 1PPJ
Gene
Ontology
ChainFunctionProcessComponent
C, P


E, R


H, U


J, W


N, A


O, B


Q, D


S, F


T, G


V, I


Primary referenceBinding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern., Huang LS, Cobessi D, Tung EY, Berry EA, J Mol Biol 2005 Aug 19;351(3):573-97. PMID:16024040
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (685 Kb) [Save to disk]
  • Biological Unit Coordinates (1pp9.pdb1.gz) 670 Kb
  • LPC: Ligand-Protein Contacts for 1PP9
  • CSU: Contacts of Structural Units for 1PP9
  • Likely Quarternary Molecular Structure file(s) for 1PP9
  • Structure Factors (2691 Kb)
  • Retrieve 1PP9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PP9 from S2C, [Save to disk]
  • Re-refined 1pp9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1PP9 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 1PP9
  • 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
  • 3D motif for 1PP9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pp9a1, region A:1-233 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9a2, region A:234-442 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9b1, region B:17-235 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9b2, region B:236-439 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9c2, region C:15-260 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9c1, region C:261-379 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9d1, region D:1-195 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9d2, region D:196-241 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9e2, region E:1-69 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9e1, region E:70-196 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1pp9g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1pp9h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1pp9i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1pp9j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1pp9n1, region N:1-233 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9n2, region N:234-442 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9o1, region O:17-235 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9o2, region O:236-439 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9p2, region P:15-260 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9p1, region P:261-379 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9q1, region Q:1-195 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9q2, region Q:196-241 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9r2, region R:1-69 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9r1, region R:70-196 [Jmol] [rasmolscript] [script source]
        - Domain d1pp9s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1pp9t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1pp9u_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1pp9v_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1pp9w_, region W [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1pp9_G] [1pp9_F] [1pp9_T] [1pp9_R] [1pp9_A] [1pp9_P] [1pp9_N] [1pp9_B] [1pp9_S] [1pp9_Q] [1pp9_H] [1pp9_O] [1pp9] [1pp9_C] [1pp9_V] [1pp9_W] [1pp9_E] [1pp9_U] [1pp9_I] [1pp9_J] [1pp9_D]
  • SWISS-PROT database: [P00125] [P00157] [P31800] [P23004] [P00126] [P00129] [P13271] [P00130] [P13272]
  • Belongs to the proton-translocating quinol:cytochrome c reductase (qcr) superfamily according to TCDB.
  • Domain organization of [CY1_BOVIN] [CYB_BOVIN] [QCR1_BOVIN] [QCR2_BOVIN] [QCR6_BOVIN] [QCR7_BOVIN] [QCR8_BOVIN] [QCR9_BOVIN] [UCRI_BOVIN] by SWISSPFAM
    • Other resources with information on 1PP9
  • Community annotation for 1PP9 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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