5EGH Hydrolase date Oct 27, 2015
title Structure Of Enpp6, A Choline-Specific Glycerophosphodiester Phosphodiesterase In Complex With Phosphocholine
authors J.Morita, K.Kano, K.Kato, H.Takita, R.Ishitani, H.Nishimasu, O.Nur J.Aoki
compound source
Molecule: Ectonucleotide Pyrophosphatasephosphodiesterase Member 6;
Chain: A, B
Fragment: Unp Residues 1-421
Synonym: Npp-6,Choline-Specific Glycerophosphodiester Phosphodiesterase,Glycerophosphocholine Cholinephosphodiest Cpde;
Ec: 3.1.4.-,3.1.4.38
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Enpp6
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
symmetry Space Group: P 1
R_factor 0.175 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.620 68.849 69.761 60.59 86.99 68.10
method X-Ray Diffractionresolution 1.80 Å
ligand EDO, FUL, NAG, PC, ZN enzyme Hydrolase E.C.3.1.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase., Morita J, Kano K, Kato K, Takita H, Sakagami H, Yamamoto Y, Mihara E, Ueda H, Sato T, Tokuyama H, Arai H, Asou H, Takagi J, Ishitani R, Nishimasu H, Nureki O, Aoki J, Sci Rep. 2016 Feb 18;6:20995. doi: 10.1038/srep20995. PMID:26888014
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (5egh.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (5egh.pdb2.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 5EGH
  • CSU: Contacts of Structural Units for 5EGH
  • Structure Factors (726 Kb)
  • Retrieve 5EGH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EGH from S2C, [Save to disk]
  • Re-refined 5egh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EGH 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 5EGH
  • 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: [5egh] [5egh_B] [5egh_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EGH
  • Community annotation for 5EGH at PDBWiki (http://pdbwiki.org)

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