1KYO Oxidoreductase Electron Transport date Feb 05, 2002
title Yeast Cytochrome Bc1 Complex With Bound Substrate Cytochrome
authors C.Lange, C.Hunte
compound source
Molecule: Ubiquinol-Cytochrome C Reductase Complex Core Pro
Chain: A, L
Fragment: Residues 27-457
Ec: 1.10.2.2
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex Core Pro
Chain: B, M
Fragment: Residues 17-368
Ec: 1.10.2.2

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Cytochrome B
Chain: C, N

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Cytochrome C1, Heme Protein
Chain: D, O
Fragment: Residues 62-309

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Iron-Sulfur Subu
Chain: E, P
Fragment: Residues 31-215
Synonym: Rieske Iron-Sulfur Protein, Risp
Ec: 1.10.2.2

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex 17 Kd Pr
Chain: F, Q
Fragment: Residues 74-147
Synonym: Mitochondrial Hinge Protein, Complex III Polypepti
Ec: 1.10.2.2

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex 14 Kd Pr
Chain: G, R
Fragment: Residues 2-127
Synonym: Complex III Subunit Vii
Ec: 1.10.2.2

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex Ubiquino Protein Qp-C;
Chain: H, S
Fragment: Residues 2-94
Synonym: Ubiquinol-Cytochrome C Reductase Complex 11 Kda Pr Complex III Subunit Viii;
Ec: 1.10.2.2

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex 7.3 Kd P
Chain: I, T
Fragment: Residues 1-57
Synonym: Complex III Polypeptide Ix
Ec: 1.10.2.2

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Heavy Chain (Vh) Of Fv-Fragment
Chain: J, U
Fragment: Residues 1-127
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm83
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pask68

Molecule: Light Chain (Vl) Of Fv-Fragment
Chain: K, V
Fragment: Residues 1-107
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm83
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pask68

Molecule: Cytochrome C, Iso-1
Chain: W

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
147.224 165.531 195.889 90.00 104.19 90.00
method X-Ray Diffractionresolution 2.97 Å
ligand FES, HEC, M3L, SMA enzyme Oxidoreductase E.C.1.10.2.2 BRENDA
note 1KYO (Molecule of the Month:pdb36, pdb137)
related structures by homologous chain: 1BAF, 1FHB, 1P84, 1RZI, 2FGW, 2PCB
Gene
Ontology
ChainFunctionProcessComponent
E, P


L, A
  • ubiquinol-cytochrome-c reduc...


  • M, B


    N, C


    O, D


    R, G


    S, H


    T, I


    W


    Primary referenceCrystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c., Lange C, Hunte C, Proc Natl Acad Sci U S A 2002 Mar 5;99(5):2800-5. PMID:11880631
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (729 Kb) [Save to disk]
  • Biological Unit Coordinates (1kyo.pdb1.gz) 707 Kb
  • LPC: Ligand-Protein Contacts for 1KYO
  • CSU: Contacts of Structural Units for 1KYO
  • Likely Quarternary Molecular Structure file(s) for 1KYO
  • Retrieve 1KYO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KYO from S2C, [Save to disk]
  • View 1KYO 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 1KYO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1KYO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kyoa2, region A:240-456 [Jmol] [rasmolscript] [script source]
        - Domain d1kyoa1, region A:27-239 [Jmol] [rasmolscript] [script source]
        - Domain d1kyob1, region B:17-218 [Jmol] [rasmolscript] [script source]
        - Domain d1kyob2, region B:219-368 [Jmol] [rasmolscript] [script source]
        - Domain d1kyoc3, region C:1-261 [Jmol] [rasmolscript] [script source]
        - Domain d1kyoc2, region C:262-385 [Jmol] [rasmolscript] [script source]
        - Domain d1kyod2, region D:261-306 [Jmol] [rasmolscript] [script source]
        - Domain d1kyod1, region D:62-260 [Jmol] [rasmolscript] [script source]
        - Domain d1kyoe2, region E:31-86 [Jmol] [rasmolscript] [script source]
        - Domain d1kyoe1, region E:87-215 [Jmol] [rasmolscript] [script source]
        - Domain d1kyof_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1kyog_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1kyoh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1kyoi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1kyoj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1kyok_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1kyol2, region L:240-456 [Jmol] [rasmolscript] [script source]
        - Domain d1kyol1, region L:27-239 [Jmol] [rasmolscript] [script source]
        - Domain d1kyom1, region M:17-218 [Jmol] [rasmolscript] [script source]
        - Domain d1kyom2, region M:219-368 [Jmol] [rasmolscript] [script source]
        - Domain d1kyon3, region N:1-261 [Jmol] [rasmolscript] [script source]
        - Domain d1kyon2, region N:262-385 [Jmol] [rasmolscript] [script source]
        - Domain d1kyoo2, region O:261-306 [Jmol] [rasmolscript] [script source]
        - Domain d1kyoo1, region O:62-260 [Jmol] [rasmolscript] [script source]
        - Domain d1kyop2, region P:31-86 [Jmol] [rasmolscript] [script source]
        - Domain d1kyop1, region P:87-215 [Jmol] [rasmolscript] [script source]
        - Domain d1kyoq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1kyor_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1kyos_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1kyot_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1kyou_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1kyov_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1kyow_, region W [Jmol] [rasmolscript] [script source]
  • Fold representative 1kyo from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1kyo_I] [1kyo_F] [1kyo_T] [1kyo_M] [1kyo_J] [1kyo_P] [1kyo_C] [1kyo_K] [1kyo_O] [1kyo_N] [1kyo_R] [1kyo_A] [1kyo] [1kyo_S] [1kyo_V] [1kyo_W] [1kyo_Q] [1kyo_H] [1kyo_L] [1kyo_D] [1kyo_B] [1kyo_U] [1kyo_G] [1kyo_E]
  • SWISS-PROT database: [P07143] [P00163] [P00044] [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] [CYC1_YEAST] [QCR1_YEAST] [QCR2_YEAST] [QCR6_YEAST] [QCR7_YEAST] [QCR8_YEAST] [QCR9_YEAST] [UCRI_YEAST] by SWISSPFAM
  • Domain found in 1KYO: [IGv ] by SMART
  • Other resources with information on 1KYO
  • Community annotation for 1KYO 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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