2VT0 Hydrolase date May 03, 2008
title X-Ray Structure Of A Conjugate With Conduritol-Beta-Epoxide Of Acid-Beta-Glucosidase Overexpressed In Cultured Plant Cells
authors B.Brumshtein, H.M.Greenblatt, Y.Shaaltiel, D.Aviezer, I.Silman, A.H.Futerman, J.L.Sussman
compound source
Molecule: Glucosylceramidase
Chain: A, B
Fragment: Tim Barrel Glucosidase, Residues 40-536
Synonym: Beta-Glucocerebrosidase, Acid Beta-Glucosidase, D-Glucosyl-N-Acylsphingosine Glucohydrolase, Glucosidase;
Ec: 3.2.1.45
Engineered: Yes
Other_details: The Enzyme Is Covalently Inhibited By Cbe
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Lysosome
Expression_system: Daucus Carota
Expression_system_taxid: 4039
symmetry Space Group: P 1 21 1
R_factor 0.152 R_Free 0.201
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.184 96.884 83.171 90.00 103.73 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand CBU, FUC, MAN, NAG, SO4 enzyme Hydrolase E.C.3.2.1.45 BRENDA
subcellular loc. Membrane localization by OPM: Lysosome membrane
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • negative regulation of inter...

  • Primary referenceAcid beta-glucosidase: insights from structural analysis and relevance to Gaucher disease therapy., Kacher Y, Brumshtein B, Boldin-Adamsky S, Toker L, Shainskaya A, Silman I, Sussman JL, Futerman AH, Biol Chem. 2008 Nov;389(11):1361-9. PMID:18783340
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (2vt0.pdb1.gz) 86 Kb
  • Biological Unit Coordinates (2vt0.pdb2.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 2VT0
  • CSU: Contacts of Structural Units for 2VT0
  • Likely Quarternary Molecular Structure file(s) for 2VT0
  • Structure Factors (447 Kb)
  • Retrieve 2VT0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VT0 from S2C, [Save to disk]
  • Re-refined 2vt0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VT0 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 2VT0
  • 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 2VT0, from MSDmotif at EBI
  • Fold representative 2vt0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vt0_B] [2vt0_A] [2vt0]
  • SWISS-PROT database: [Q9BDT0]
  • Domain organization of [GLCM_PANTR] by SWISSPFAM
  • Alignments of the sequence of 2VT0 with the sequences similar proteins can be viewed for 2VT0's classification [GLCM_PANTR] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [GLCM_PANTR] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VT0
  • Community annotation for 2VT0 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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