3WEB Lipid Binding Protein date Jul 02, 2013
title Crystal Structure Of A Niemann-Pick Type C2 Protein From Jap Carpenter Ant In Complex With Oleic Acid
authors Z.Fujimoto, W.Tsuchiya, Y.Ishida, T.Yamazaki
compound source
Molecule: Niemann-Pick Type C2 Protein
Chain: A
Engineered: Yes
 Organism_scientific: Camponotus Japonicus
Organism_taxid: 84547
Gene: Cjapnpc2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-22b
symmetry Space Group: P 21 21 2
R_factor 0.216 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.849 103.177 39.311 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand OLA enzyme
Primary referenceNiemann-Pick type C2 protein mediating chemical communication in the worker ant., Ishida Y, Tsuchiya W, Fujii T, Fujimoto Z, Miyazawa M, Ishibashi J, Matsuyama S, Ishikawa Y, Yamazaki T, Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3847-52. doi:, 10.1073/pnas.1323928111. Epub 2014 Feb 24. PMID:24567405
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (3web.pdb1.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 3WEB
  • CSU: Contacts of Structural Units for 3WEB
  • Structure Factors (364 Kb)
  • Retrieve 3WEB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WEB from S2C, [Save to disk]
  • Re-refined 3web structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3WEB 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 3WEB
  • 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 3WEB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3web_A] [3web]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3WEB: [ML ] by SMART
    • Other resources with information on 3WEB
  • Community annotation for 3WEB at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science