2OSX Hydrolase date Feb 06, 2007
title Endo-Glycoceramidase II From Rhodococcus Sp.: Ganglioside Gm
authors M.E.C.Caines, N.C.J.Strynadka
compound source
Molecule: Endoglycoceramidase II
Chain: A
Ec: 3.2.1.123
Engineered: Yes
Mutation: Yes
Organism_scientific: Rhodococcus Sp.
Organism_taxid: 1831
Strain: M-777
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(Tuner)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a(+)
symmetry Space Group: C 1 2 1
R_factor 0.121 R_Free 0.139
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.801 61.984 102.846 90.00 112.25 90.00
method X-Ray Diffractionresolution 1.10 Å
ligand 16C, BGC, GAL, GOL, NA, SIA enzyme Hydrolase E.C.3.2.1.123 BRENDA
note 2OSX is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms., Caines ME, Vaughan MD, Tarling CA, Hancock SM, Warren RA, Withers SG, Strynadka NC, J Biol Chem. 2007 May 11;282(19):14300-8. Epub 2007 Feb 28. PMID:17329247
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (171 Kb) [Save to disk]
  • Biological Unit Coordinates (2osx.pdb1.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 2OSX
  • CSU: Contacts of Structural Units for 2OSX
  • Likely Quarternary Molecular Structure file(s) for 2OSX
  • Structure Factors (1278 Kb)
  • Retrieve 2OSX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OSX from S2C, [Save to disk]
  • Re-refined 2osx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OSX 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 2OSX
  • 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
  • 3D motif for 2OSX, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2osx] [2osx_A]
  • SWISS-PROT database: [O33853]
  • Domain organization of [O33853_RHOSO] by SWISSPFAM
  • Other resources with information on 2OSX
  • Community annotation for 2OSX 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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