5TCD Hydrolase date Sep 14, 2016
title Human Alkaline Sphingomyelinase (Enpp7) In Complex With Phos
authors A.Gorelik, F.Liu, K.Illes, B.Nagar
compound source
Molecule: Ectonucleotide Pyrophosphatasephosphodiesterase Member 7;
Chain: A
Fragment: Unp Residues 22-433
Synonym: Npp-7,Alkaline Sphingomyelin Phosphodiesterase,Int Alkaline Sphingomyelinase,Alk-Smase;
Ec: 3.1.4.12
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Enpp7, Unq3077pro9912
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 31 2 1
R_factor 0.173 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.223 104.223 113.893 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand BMA, FUC, IOD, NA, NAG, PC, ZN enzyme Hydrolase E.C.3.1.4.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal Structure of the Human Alkaline Sphingomyelinase Provides Insights into Substrate Recognition., Gorelik A, Liu F, Illes K, Nagar B, J Biol Chem. 2017 Mar 14. pii: jbc.M116.769273. doi: 10.1074/jbc.M116.769273. PMID:28292932
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (207 Kb) [Save to disk]
  • Biological Unit Coordinates (5tcd.pdb1.gz) 199 Kb
  • LPC: Ligand-Protein Contacts for 5TCD
  • CSU: Contacts of Structural Units for 5TCD
  • Structure Factors (287 Kb)
  • Retrieve 5TCD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TCD from S2C, [Save to disk]
  • Re-refined 5tcd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5TCD 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 5TCD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tcd] [5tcd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5TCD
  • Community annotation for 5TCD at PDBWiki (http://pdbwiki.org)

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