4WGK Hydrolase date Sep 18, 2014
title Crystal Structure Of Human Neutral Ceramidase With Zn-Bound
authors M.V.Airola, M.J.Pulkoski-Gross, L.M.Obeid, Y.A.Hannun
compound source
Molecule: Neutral Ceramidase
Chain: A, B
Synonym: Ncdase, Acylsphingosine Deacylase 2, Bcdase, Lcdas Acylsphingosine Amidohydrolase 2, Non-Lysosomal Ceramidase;
Ec: 3.5.1.23
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Asah2, Hnac1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
symmetry Space Group: P 1 21 1
R_factor 0.178 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.480 156.630 80.330 90.00 108.04 90.00
method X-Ray Diffractionresolution 2.58 Å
ligand BMA, CA, CIT, CL, EDO, NAG, PO4, ZN enzyme Hydrolase E.C.3.5.1.23 BRENDA
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase., Airola MV, Allen WJ, Pulkoski-Gross MJ, Obeid LM, Rizzo RC, Hannun YA, Structure. 2015 Aug 4;23(8):1482-91. doi: 10.1016/j.str.2015.06.013. Epub 2015, Jul 16. PMID:26190575
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (456 Kb) [Save to disk]
  • Biological Unit Coordinates (4wgk.pdb1.gz) 226 Kb
  • Biological Unit Coordinates (4wgk.pdb2.gz) 225 Kb
  • LPC: Ligand-Protein Contacts for 4WGK
  • CSU: Contacts of Structural Units for 4WGK
  • Structure Factors (918 Kb)
  • Retrieve 4WGK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4WGK from S2C, [Save to disk]
  • Re-refined 4wgk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4WGK 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 4WGK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 4wgk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4wgk] [4wgk_B] [4wgk_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4WGK
  • Community annotation for 4WGK at PDBWiki (http://pdbwiki.org)

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