1OYD Membrane Protein date Apr 03, 2003
title Structural Basis Of Multiple Binding Capacity Of The Acrb Mu Efflux Pump
authors E.W.Yu, G.Medermott, H.I.Zgurskaya, H.Nikaido, D.E.Koshland Jr.
compound source
Molecule: Acriflavine Resistance Protein B
Chain: A
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Acrb Or Acre Or B0462
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3 2
R_factor 0.284 R_Free 0.338
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.767 144.767 517.891 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.80 Å
ligand DEQ enzyme
note 1OYD (Molecule of the Month:pdb95)
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump., Yu EW, McDermott G, Zgurskaya HI, Nikaido H, Koshland DE Jr, Science 2003 May 9;300(5621):976-80. PMID:12738864
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk]
  • Biological Unit Coordinates (1oyd.pdb1.gz) 454 Kb
  • LPC: Ligand-Protein Contacts for 1OYD
  • CSU: Contacts of Structural Units for 1OYD
  • Likely Quarternary Molecular Structure file(s) for 1OYD
  • Structure Factors (306 Kb)
  • Retrieve 1OYD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OYD from S2C, [Save to disk]
  • Re-refined 1oyd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1OYD 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 1OYD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1OYD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1oyda2, region A:135-181,A:274-330 [Jmol] [rasmolscript] [script source]
        - Domain d1oyda5, region A:182-273 [Jmol] [rasmolscript] [script source]
        - Domain d1oyda1, region A:38-134 [Jmol] [rasmolscript] [script source]
        - Domain d1oyda8, region A:513-566,A:869-1036 [Jmol] [rasmolscript] [script source]
        - Domain d1oyda3, region A:567-673 [Jmol] [rasmolscript] [script source]
        - Domain d1oyda4, region A:674-724,A:813-859 [Jmol] [rasmolscript] [script source]
        - Domain d1oyda7, region A:7-37,A:331-498 [Jmol] [rasmolscript] [script source]
        - Domain d1oyda6, region A:725-812 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1oyd] [1oyd_A]
  • SWISS-PROT database: [P31224]
  • Belongs to the resistance-nodulation-cell division (rnd) superfamily according to TCDB.
  • Domain organization of [ACRB_ECOLI] by SWISSPFAM
    • Other resources with information on 1OYD
  • Community annotation for 1OYD 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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