4Q65 Transport Protein date Apr 21, 2014
title Structure Of The E. Coli Peptide Transporter Ybgh
authors C.Zhang, Y.Zhao, G.Mao, M.Liu, X.Wang
compound source
Molecule: Dipeptide Permease D
Chain: A
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: Dtpd, Ybgh, B0709, Jw0699
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.258 R_Free 0.316
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.035 109.448 76.659 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
Gene
Ontology
ChainFunctionProcessComponent
A
  • peptide:proton symporter act...
  • tripeptide transporter activ...


  • Primary referenceCrystal Structure of the E. coli Peptide Transporter YbgH., Zhao Y, Mao G, Liu M, Zhang L, Wang X, Zhang XC, Structure. 2014 Aug 5;22(8):1152-60. doi: 10.1016/j.str.2014.06.008. Epub 2014, Jul 24. PMID:25066136
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (4q65.pdb1.gz) 144 Kb
  • CSU: Contacts of Structural Units for 4Q65
  • Structure Factors (465 Kb)
  • Retrieve 4Q65 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Q65 from S2C, [Save to disk]
  • Re-refined 4q65 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q65 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 4Q65
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4Q65, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q65] [4q65_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4Q65
  • Community annotation for 4Q65 at PDBWiki (http://pdbwiki.org)

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