3VR8 Oxidoreductase date Apr 07, 2012
title Mitochondrial Rhodoquinol-Fumarate Reductase From The Parasi Nematode Ascaris Suum
authors H.Shimizu, T.Shiba, D.K.Inaoka, A.Osanai, K.Kita, K.Sakamoto, S.Ha
compound source
Molecule: Flavoprotein Subunit Of Complex II
Chain: A, E
Synonym: Rhodoquinol-Fumarate Reductase Fp Subunit
 Organism_scientific: Ascaris Suum
Organism_common: Pig Roundworm
Organism_taxid: 6253
Organelle: Mitochondria

Molecule: Iron-Sulfur Subunit Of Succinate Dehydrogenase
Chain: B, F
Synonym: Rhodoquinol-Fumarate Reductase Ip Subunit
Organism_scientific: Ascaris Suum
Organism_common: Pig Roundworm
Organism_taxid: 6253
Organelle: Mitochondria

Molecule: Cytochrome B-Large Subunit
Chain: C, G
Synonym: Rhodoquinol-Fumarate Reductase Cybl Subunit
Organism_scientific: Ascaris Suum
Organism_common: Pig Roundworm
Organism_taxid: 6253
Organelle: Mitochondria

Molecule: Succinate Dehydrogenase [Ubiquinone] Cytochrome B Subunit, Mitochondrial;
Chain: D, H
Synonym: Cybs, Cytochrome B558 Small Subunit, Succinate-Ubi Reductase Membrane Anchor Subunit, Rhodoquinol-Fumarate Red Cybs Subunit
Organism_scientific: Ascaris Suum
Organism_common: Pig Roundworm
Organism_taxid: 6253
Organelle: Mitochondria
symmetry Space Group: P 21 21 21
R_factor 0.231 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
123.707 129.090 221.167 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand EPH, F3S, FAD, FES, HEM, MLI, RQX, SF4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G
  • electron transfer activity


    • F, B
  • electron transfer activity


    • H, D


    Primary referenceCrystal structure of mitochondrial quinol-fumarate reductase from the parasitic nematode Ascaris suum., Shimizu H, Osanai A, Sakamoto K, Inaoka DK, Shiba T, Harada S, Kita K, J Biochem. 2012 Jun;151(6):589-92. Epub 2012 May 9. PMID:22577165
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (371 Kb) [Save to disk]
  • Biological Unit Coordinates (3vr8.pdb1.gz) 184 Kb
  • Biological Unit Coordinates (3vr8.pdb2.gz) 184 Kb
  • LPC: Ligand-Protein Contacts for 3VR8
  • CSU: Contacts of Structural Units for 3VR8
  • Structure Factors (1158 Kb)
  • Retrieve 3VR8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VR8 from S2C, [Save to disk]
  • Re-refined 3vr8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3VR8 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 3VR8
  • 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 3VR8, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vr8_G] [3vr8_H] [3vr8_C] [3vr8_F] [3vr8] [3vr8_B] [3vr8_D] [3vr8_E] [3vr8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3VR8
  • Community annotation for 3VR8 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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