2HPY Signaling Protein date Jul 18, 2006
title Crystallographic Model Of Lumirhodopsin
authors H.Nakamichi, T.Okada
compound source
Molecule: Rhodopsin
Chain: A, B
 Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
symmetry Space Group: P 41
R_factor 0.218 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.720 96.720 150.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ACE, BMA, HG, HTG, HTO, MAN, NAG, PLM, RET, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceLocal peptide movement in the photoreaction intermediate of rhodopsin., Nakamichi H, Okada T, Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12729-34. Epub 2006 Aug 14. PMID:16908857
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk]
  • Biological Unit Coordinates (2hpy.pdb1.gz) 119 Kb
  • Biological Unit Coordinates (2hpy.pdb2.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 2HPY
  • CSU: Contacts of Structural Units for 2HPY
  • Likely Quarternary Molecular Structure file(s) for 2HPY
  • Structure Factors (251 Kb)
  • Retrieve 2HPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HPY from S2C, [Save to disk]
    • View 2HPY 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 2HPY
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2HPY, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hpy_A] [2hpy_B] [2hpy]
  • SWISS-PROT database: [P02699]
  • Domain organization of [OPSD_BOVIN] by SWISSPFAM
    • Other resources with information on 2HPY
  • Community annotation for 2HPY 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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