5XSZ Membrane Protein date Jun 16, 2017
title Crystal Structure Of Zebrafish Lysophosphatidic Acid Recepto
authors R.Taniguchi, T.Nishizawa, R.Ishitani, O.Nureki
compound source
Molecule: Lysophosphatidic Acid Receptor 6a,Endolysin, Lysophosphatidic Acid Receptor 6a;
Chain: A
Synonym: Zgc:153784,Zgc:153784 Protein,Lysis Protein,Lysozy Muramidase;
Ec: 3.2.1.17
Engineered: Yes
Mutation: Yes
Other_details: Chimera Protein Of Unp Residues 1-227 From Lysophosphatidic Acid Receptor 6a (Q08bg4), Unp Residues 2- Endolysin (P00720),Unp Residues 233-312 From Lysophosphatid Receptor 6a (Q08bg4).
Organism_scientific: Danio Rerio, Enterobacteria Phage T4
Organism_common: Zebrafish
Organism_taxid: 7955, 10665
Gene: Lpar6a, Lpar6, Zgc:153784
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 21
R_factor 0.236 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.880 65.020 160.650 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand OLC enzyme Hydrolase E.C.3.2.1.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural insights into ligand recognition by the lysophosphatidic acid receptor LPA6., Taniguchi R, Inoue A, Sayama M, Uwamizu A, Yamashita K, Hirata K, Yoshida M, Tanaka Y, Kato HE, Nakada-Nakura Y, Otani Y, Nishizawa T, Doi T, Ohwada T, Ishitani R, Aoki J, Nureki O, Nature. 2017 Aug 17;548(7667):356-360. doi: 10.1038/nature23448. Epub 2017 Aug 9. PMID:28792932
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (5xsz.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 5XSZ
  • CSU: Contacts of Structural Units for 5XSZ
  • Structure Factors (159 Kb)
  • Retrieve 5XSZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XSZ from S2C, [Save to disk]
  • View 5XSZ 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 5XSZ
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xsz_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XSZ
  • Community annotation for 5XSZ at PDBWiki (http://pdbwiki.org)

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