3VVK Membrane Protein date Jul 26, 2012
title An M-Like Reaction State Of The Azide-Bound Purple Form Of P Halorhodopsin
authors T.Kouyama, T.Nakanishi
compound source
Molecule: Halorhodopsin
Chain: A, B, C, D, E, F
Organism_scientific: Natronomonas Pharaonis
Organism_taxid: 2257
Strain: Mk-1
Other_details: Strain Mk-1 Was A Halorhodopsin-Overproducin Generated From Type Strain D2160t.
symmetry Space Group: C 1 2 1
R_factor 0.211 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
153.850 97.900 101.020 90.00 128.53 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 22B, AZI, BNG, L3P, RET enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B
  • ion channel activity


  • Primary referenceLarge deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide., Nakanishi T, Kanada S, Murakami M, Ihara K, Kouyama T, Biophys J. 2013 Jan 22;104(2):377-85. doi: 10.1016/j.bpj.2012.12.018. PMID:23442859
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (3vvk.pdb1.gz) 122 Kb
  • Biological Unit Coordinates (3vvk.pdb2.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 3VVK
  • CSU: Contacts of Structural Units for 3VVK
  • Structure Factors (458 Kb)
  • Retrieve 3VVK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VVK from S2C, [Save to disk]
  • Re-refined 3vvk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VVK 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 3VVK
  • 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 3VVK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vvk_C] [3vvk_E] [3vvk_A] [3vvk_D] [3vvk_F] [3vvk] [3vvk_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VVK: [Bac_rhodopsin ] by SMART
  • Other resources with information on 3VVK
  • Community annotation for 3VVK at PDBWiki (http://pdbwiki.org)

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