3NKM Crystal structure of mouse autotaxin date
authors Nishimasu, H., Ishitani, R., Mihara, E., Takagi, J., Aoki, J., Nureki, O.
compound source
R_Free 0.2126
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.00
ligand BMA, CA, EDO, K, MAN, NA, NAG, NKP, SCN, SO4, ZN enzyme
  • 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] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (3nkm.pdb1.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 3NKM
  • CSU: Contacts of Structural Units for 3NKM
  • Structure Factors (431 Kb)
  • Retrieve 3NKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NKM from S2C, [Save to disk]
  • Re-refined 3nkm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NKM 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 3NKM
  • 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 3NKM, from MSDmotif at EBI
  • Fold representative 3nkm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nkm_A] [3nkm]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3NKM: [Endonuclease_NS] [NUC] [SO ] by SMART
  • Other resources with information on 3NKM
  • Community annotation for 3NKM 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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