authors Okada, T., Palczewski, K., Stenkamp, R.E., Miyano, M.
compound source
R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand HG, MAN, NAG, RET, ZN enzyme
note 1F88 (Molecule of the Month:pdb27, pdb58, pdb66, pdb100, pdb147)
related structures by homologous chain: 1EDS, 1EDV, 1EDX, 1HZX
A, B

Primary referenceCrystal structure of rhodopsin: A G protein-coupled receptor., Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M, Science 2000 Aug 4;289(5480):739-45. PMID:10926528
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (1f88.pdb1.gz) 105 Kb
  • Biological Unit Coordinates (1f88.pdb2.gz) 56 Kb
  • Biological Unit Coordinates (1f88.pdb3.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 1F88
  • CSU: Contacts of Structural Units for 1F88
  • Likely Quarternary Molecular Structure file(s) for 1F88
  • Retrieve 1F88 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1F88 from S2C, [Save to disk]
  • View 1F88 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 1F88
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1F88, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1f88a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1f88b_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1f88] [1f88_A] [1f88_B]
  • SWISS-PROT database: [P02699]
  • Domain organization of [OPSD_BOVIN] by SWISSPFAM
  • Other resources with information on 1F88
  • Community annotation for 1F88 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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