2ZIY Signaling Protein date Feb 27, 2008
title Crystal Structure Of Squid Rhodopsin
authors M.Miyano, T.Shimamura
compound source
Molecule: Rhodopsin
Chain: A
Fragment: Truncation Of C-Terminal Polypro By V8-Protease,
Residues 2-373: Val18ile Confirmed By Ms
 Organism_scientific: Todarodes Pacificus
Organism_common: Japanese Flying Squid
symmetry Space Group: C 2 2 21
R_factor 0.302 R_Free 0.330
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.319 108.746 142.165 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.70 Å
ligand PLM, RET enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of squid rhodopsin with intracellularly extended cytoplasmic region., Shimamura T, Hiraki K, Takahashi N, Hori T, Ago H, Masuda K, Takio K, Ishiguro M, Miyano M, J Biol Chem. 2008 Jun 27;283(26):17753-6. Epub 2008 May 6. PMID:18463093
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (2ziy.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (2ziy.pdb2.gz) 106 Kb
  • LPC: Ligand-Protein Contacts for 2ZIY
  • CSU: Contacts of Structural Units for 2ZIY
  • Likely Quarternary Molecular Structure file(s) for 2ZIY
  • Structure Factors (43 Kb)
  • Retrieve 2ZIY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZIY from S2C, [Save to disk]
  • Re-refined 2ziy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2ZIY 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 2ZIY
  • 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 2ZIY, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ziy_A] [2ziy]
  • SWISS-PROT database: [P31356]
  • Domain organization of [OPSD_TODPA] by SWISSPFAM
    • Other resources with information on 2ZIY
  • Community annotation for 2ZIY 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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