4IKV Transport Protein date Dec 28, 2012
title Crystal Structure Of Peptide Transporter Pot
authors S.Doki, H.E.Kato, R.Ishitani, O.Nureki
compound source
Molecule: Di-Tripeptide Abc Transporter (Permease)
Chain: A
Engineered: Yes
Organism_scientific: Geobacillus Kaustophilus
Organism_taxid: 1462
Strain: Bd53
Gene: Gk2020
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C41(De3)Delta-Acrb
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcgfp-Bc
symmetry Space Group: P 1 21 1
R_factor 0.181 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.761 94.917 57.253 90.00 111.10 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand OLA, OLB, PG4, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT., Doki S, Kato HE, Solcan N, Iwaki M, Koyama M, Hattori M, Iwase N, Tsukazaki T, Sugita Y, Kandori H, Newstead S, Ishitani R, Nureki O, Proc Natl Acad Sci U S A. 2013 Jun 24. PMID:23798427
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (161 Kb) [Save to disk]
  • Biological Unit Coordinates (4ikv.pdb1.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 4IKV
  • CSU: Contacts of Structural Units for 4IKV
  • Structure Factors (246 Kb)
  • Retrieve 4IKV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IKV from S2C, [Save to disk]
  • Re-refined 4ikv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IKV 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 4IKV
  • 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 4IKV, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ikv_A] [4ikv]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4IKV
  • Community annotation for 4IKV at PDBWiki (http://pdbwiki.org)

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