1UCQ Proton Transport date Apr 17, 2003
title Crystal Structure Of The L Intermediate Of Bacteriorhodopsin
authors T.Kouyama, T.Nishikawa, T.Tokuhisa, H.Okumura
compound source
Molecule: Bacteriorhodopsin
Chain: A
Organism_scientific: Halobacterium Salinarum
Organism_taxid: 2242
Strain: Jw3
symmetry Space Group: P 6 2 2
R_factor 0.300 R_Free 0.333
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.300 102.300 112.300 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand GAL, GLC, L2P, L3P, MAN, RET enzyme
related structures by homologous chain: 1AP9, 1TN0
Gene
Ontology
ChainFunctionProcessComponent
A
  • ion channel activity


  • Primary referenceCrystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle., Kouyama T, Nishikawa T, Tokuhisa T, Okumura H, J Mol Biol 2004 Jan 9;335(2):531-46. PMID:14672661
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (1ucq.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 1UCQ
  • CSU: Contacts of Structural Units for 1UCQ
  • Likely Quarternary Molecular Structure file(s) for 1UCQ
  • Structure Factors (159 Kb)
  • Retrieve 1UCQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UCQ from S2C, [Save to disk]
  • Re-refined 1ucq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1UCQ 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 1UCQ
  • 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 1UCQ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ucqa_, 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: [1ucq_A] [1ucq]
  • 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 1UCQ: [Bac_rhodopsin ] by SMART
  • Other resources with information on 1UCQ
  • Community annotation for 1UCQ 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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