5IXM Transport Protein date Mar 23, 2016
title The Lps Transporter Lptde From Yersinia Pestis, Core Complex
authors I.Botos, S.J.Mayclin, J.G.Mccarthy, S.K.Buchanan
compound source
Molecule: Lps-Assembly Protein Lptd
Chain: A, C, E, G
Fragment: Unp Residues 225-780
Engineered: Yes
Organism_scientific: Yersinia Pestis
Organism_taxid: 632
Gene: Lptd, Imp, Osta, Ypo0495, Y3680, Yp_3684
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Lps-Assembly Lipoprotein Lpte
Chain: B, D, F, H
Fragment: Unp Residues 21-207
Engineered: Yes

Organism_scientific: Yersinia Pestis
Organism_taxid: 632
Gene: Lpte, Rlpb, Ypo2609, Y1183, Yp_1104
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.212 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.892 176.354 143.848 90.00 96.11 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand C8E enzyme
Gene YP ; YP
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


Primary referenceStructural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens., Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, Buchanan SK, Structure. 2016 May 3. pii: S0969-2126(16)30043-0. doi:, 10.1016/j.str.2016.03.026. PMID:27161977
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (468 Kb) [Save to disk]
  • Biological Unit Coordinates (5ixm.pdb1.gz) 119 Kb
  • Biological Unit Coordinates (5ixm.pdb2.gz) 121 Kb
  • Biological Unit Coordinates (5ixm.pdb3.gz) 116 Kb
  • Biological Unit Coordinates (5ixm.pdb4.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 5IXM
  • CSU: Contacts of Structural Units for 5IXM
  • Structure Factors (1885 Kb)
  • Retrieve 5IXM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IXM from S2C, [Save to disk]
  • Re-refined 5ixm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IXM 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 5IXM
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ixm_D] [5ixm_C] [5ixm_F] [5ixm_G] [5ixm] [5ixm_E] [5ixm_B] [5ixm_A] [5ixm_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5IXM
  • Community annotation for 5IXM at PDBWiki (http://pdbwiki.org)

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