1NTK Oxidoreductase date Jan 30, 2003
title Crystal Structure Of Mitochondrial Cytochrome Bc1 In Complex Antimycin A1
authors X.Gao, X.Wen, L.Esser, B.Quinn, L.Yu, C.A.Yu, D.Xia
compound source
Molecule: Ubiquinol-Cytochrome C Reductase Complex Core Pro Mitochondrial;
Chain: A
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
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
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Cytochrome C1
Chain: D
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Iron-Sulfur Subu Mitochondrial;
Chain: E
Synonym: Rieske Iron-Sulfur Protein, Risp
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
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
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
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 8 Kda Protein
Chain: I
Synonym: Complex III Subunit Ix
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
Synonym: Cytochrome C1, Nonheme 7 Kda Protein; Complex III
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913

Molecule: Ubiquinol-Cytochrome C Reductase Complex 6.4 Kda
Chain: K
Synonym: Complex III Subunit Xi
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
symmetry Space Group: I 41 2 2
R_factor 0.233 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
153.785 153.785 592.498 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand AY1, FES, HEM enzyme Oxidoreductase E.C.1.10.2.2 BRENDA
related structures by homologous chain: 1NTM, 1NTZ
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K
  • ubiquinol-cytochrome-c reduc...


    • Primary referenceStructural basis for the quinone reduction in the bc1 complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc1 with bound substrate and inhibitors at the Qi site., Gao X, Wen X, Esser L, Quinn B, Yu L, Yu CA, Xia D, Biochemistry 2003 Aug 5;42(30):9067-80. PMID:12885240
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (358 Kb) [Save to disk]
  • Biological Unit Coordinates (1ntk.pdb1.gz) 682 Kb
  • LPC: Ligand-Protein Contacts for 1NTK
  • CSU: Contacts of Structural Units for 1NTK
  • Likely Quarternary Molecular Structure file(s) for 1NTK
  • Retrieve 1NTK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NTK from S2C, [Save to disk]
    • View 1NTK 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 1NTK
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1NTK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ntka1, region A:1-233 [Jmol] [rasmolscript] [script source]
        - Domain d1ntka2, region A:234-446 [Jmol] [rasmolscript] [script source]
        - Domain d1ntkb1, region B:17-235 [Jmol] [rasmolscript] [script source]
        - Domain d1ntkb2, region B:236-439 [Jmol] [rasmolscript] [script source]
        - Domain d1ntkc2, region C:2-260 [Jmol] [rasmolscript] [script source]
        - Domain d1ntkc1, region C:261-379 [Jmol] [rasmolscript] [script source]
        - Domain d1ntkd1, region D:1-195 [Jmol] [rasmolscript] [script source]
        - Domain d1ntkd2, region D:196-241 [Jmol] [rasmolscript] [script source]
        - Domain d1ntke2, region E:1-69 [Jmol] [rasmolscript] [script source]
        - Domain d1ntke1, region E:70-196 [Jmol] [rasmolscript] [script source]
        - Domain d1ntkf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1ntkg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1ntkh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1ntki_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1ntkj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1ntkk_, region K [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: [1ntk_G] [1ntk_I] [1ntk_A] [1ntk_J] [1ntk_B] [1ntk_F] [1ntk_K] [1ntk] [1ntk_H] [1ntk_E] [1ntk_D] [1ntk_C]
  • SWISS-PROT database: [P00125] [P00157] [P07552] [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] [QCR10_BOVIN] [QCR1_BOVIN] [QCR2_BOVIN] [QCR6_BOVIN] [QCR7_BOVIN] [QCR8_BOVIN] [QCR9_BOVIN] [UCRI_BOVIN] by SWISSPFAM
    • Other resources with information on 1NTK
  • Community annotation for 1NTK 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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