1DZE Bacteriorhodopsin date Feb 25, 2000
title Structure Of The M Intermediate Of Bacteriorhodopsin Trapped
authors K.Takeda, Y.Matsui, H.Sato, T.Hino, E.Kanamori, H.Okumura, T.Yaman T.Iizuka, N.Kamiya, S.Adachi, T.Kouyama
compound source
Molecule: Bacteriorhodopsin (M Intermediate)
Chain: A
Other_details: 5 Lipids And 18 Water Molecules
Organism_scientific: Halobacterium Salinarium
Organism_taxid: 2242
Strain: Jw3
Cellular_location: Cell Membrane
Other_details: Halobacterium Salinarium
symmetry Space Group: P 6 2 2
R_factor 0.257 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.400 102.400 112.300 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand GAL, GLC, L1P, L2P, L3P, L4P, MAN, RET enzyme
note 1DZE (Molecule of the Month:pdb27)
related structures by homologous chain: 1IXF, 1QM8
Gene
Ontology
ChainFunctionProcessComponent
A
  • ion channel activity


  • Primary referenceCrystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix., Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T, J Mol Biol. 2004 Aug 20;341(4):1023-37. PMID:15328615
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (1dze.pdb1.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 1DZE
  • CSU: Contacts of Structural Units for 1DZE
  • Likely Quarternary Molecular Structure file(s) for 1DZE
  • Retrieve 1DZE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DZE from S2C, [Save to disk]
  • View 1DZE 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 1DZE
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1DZE, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dzea_, region A [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: [1dze_A] [1dze]
  • SWISS-PROT database: [P02945]
  • Belongs to the ion-translocating microbial rhodopsin (mr) family according to TCDB.
  • Domain organization of [BACR_HALSA] by SWISSPFAM
  • Domain found in 1DZE: [Bac_rhodopsin ] by SMART
  • Other resources with information on 1DZE
  • Community annotation for 1DZE 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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