5KKZ Oxidoreductase date Jun 23, 2016
title Rhodobacter Sphaeroides Bc1 With Famoxadone
authors D.Xia, L.Esser, F.Zhou, W.K.Tang, C.A.Yu
compound source
Molecule: Cytochrome B
Chain: A, E, K, O
Engineered: Yes
Organism_scientific: Rhodobacter Sphaeroides
Organism_taxid: 1063
Gene: Petb, Fbcb
Expression_system: Rhodobacter Sp.
Expression_system_taxid: 1062

Molecule: Cytochrome C1
Chain: B, F, L, P
Engineered: Yes

Organism_scientific: Rhodobacter Sphaeroides
Organism_taxid: 1063
Gene: Petc, Fbcc
Expression_system: Rhodobacter Sp.
Expression_system_taxid: 1062

Molecule: Ubiquinol-Cytochrome C Reductase Iron-Sulfur Subu
Chain: C, G, M, Q
Synonym: Rieske Iron-Sulfur Protein,Risp
Ec: 1.10.2.2
Engineered: Yes

Organism_scientific: Rhodobacter Sphaeroides
Organism_taxid: 1063
Gene: Peta, Fbcf
Expression_system: Rhodobacter Sp.
Expression_system_taxid: 1062
symmetry Space Group: P 1
R_factor 0.215 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.773 128.277 128.283 63.92 88.63 63.38
method X-Ray Diffractionresolution 2.97 Å
ligand ASC, BOG, FES, FMX, HEC, HEM, LOP, SR enzyme Oxidoreductase E.C.1.10.2.2 BRENDA
subcellular loc. Membrane localization by OPM: Bacterial Gram-negative inner membrane
Gene
Ontology
ChainFunctionProcessComponent
A, O, K, E
  • ubiquinol-cytochrome-c reduc...


  • F, P, B, L


    Q, M, C, G
  • ubiquinol-cytochrome-c reduc...


  • Primary referenceHydrogen Bonding to the substrate is not required for Rieske iron-sulfur protein docking to the quinol oxidation site of complex III., Esser L, Zhou F, Zhou Y, Xiao Y, Tang WK, Yu CA, Qin Z, Xia D, J Biol Chem. 2016 Oct 7. pii: jbc.M116.744391. PMID:27758861
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1752 Kb) [Save to disk]
  • Biological Unit Coordinates (5kkz.pdb1.gz) 865 Kb
  • Biological Unit Coordinates (5kkz.pdb2.gz) 867 Kb
  • LPC: Ligand-Protein Contacts for 5KKZ
  • CSU: Contacts of Structural Units for 5KKZ
  • Structure Factors (1455 Kb)
  • Retrieve 5KKZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KKZ from S2C, [Save to disk]
  • Re-refined 5kkz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KKZ 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 5KKZ
  • 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
  • Fold representative 5kkz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kkz_M] [5kkz_F] [5kkz_L] [5kkz_B] [5kkz_C] [5kkz_Q] [5kkz_A] [5kkz] [5kkz_O] [5kkz_E] [5kkz_K] [5kkz_P] [5kkz_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5KKZ
  • Community annotation for 5KKZ at PDBWiki (http://pdbwiki.org)

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