3NKR Crystal structure of mouse autotaxin in complex with 22:6-LPA date
authors Nishimasu, H., Ishitani, R., Mihara, E., Takagi, J., Aoki, J., Nureki, O.
compound source
symmetry
R_factor
R_Free 0.2198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.70
ligand BMA, CA, EDO, K, MAN, NA, NAG, NKR, SCN, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • phosphodiesterase I activity...
  • scavenger receptor activity


  • Primary referenceCrystal structure of autotaxin and insight into GPCR activation by lipid mediators., Nishimasu H, Okudaira S, Hama K, Mihara E, Dohmae N, Inoue A, Ishitani R, Takagi J, Aoki J, Nureki O, Nat Struct Mol Biol. 2011 Feb;18(2):205-12. doi: 10.1038/nsmb.1998. Epub 2011 Jan, 16. PMID:21240269
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (3nkr.pdb1.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 3NKR
  • CSU: Contacts of Structural Units for 3NKR
  • Structure Factors (1498 Kb)
  • Retrieve 3NKR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NKR from S2C, [Save to disk]
  • Re-refined 3nkr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NKR 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 3NKR
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3NKR, from MSDmotif at EBI
  • Fold representative 3nkr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nkr] [3nkr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3NKR: [Endonuclease_NS] [NUC] [SO ] by SMART
  • Other resources with information on 3NKR
  • Community annotation for 3NKR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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