2V3D Hydrolase date Jun 17, 2007
title Acid-Beta-Glucosidase With N-Butyl-Deoxynojirimycin
authors B.Brumshtein, H.M.Greenblatt, T.D.Butters, Y.Shaaltiel, D.Aviezer, I.Silman, A.H.Futerman, J.L.Sussman
compound source
Molecule: Glucosylceramidase
Chain: A, B
Synonym: Beta-Glucocerebrosidase, Acid-Beta-Glucosidase, D-Glucosyl-N-Acylsphingosine Glucohydrolase, Alglucerase, Imiglucerase;
Ec: 3.2.1.45
Engineered: Yes
Other_details: Nb-Dnj Inhibitor In The Active Site
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Daucus Carota
Expression_system_taxid: 4039
symmetry Space Group: P 1 21 1
R_factor 0.154 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.993 97.210 82.406 90.00 102.91 90.00
method X-Ray Diffractionresolution 1.96 Å
ligand BMA, FUC, NAG, NBV, SO4 BindingDB enzyme Hydrolase E.C.3.2.1.45 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • negative regulation of inter...

  • Primary referenceCrystal structures of complexes of N-butyl- and N-nonyl-deoxynojirimycin bound to acid-beta -glucosidase: Insights into the mechanism of chemical chaperone action in gaucher disease., Brumshtein B, Greenblatt HM, Butters TD, Shaaltiel Y, Aviezer D, Silman I, Futerman AH, Sussman JL, J Biol Chem. 2007 Jul 31;. PMID:17666401
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (188 Kb) [Save to disk]
  • Biological Unit Coordinates (2v3d.pdb1.gz) 93 Kb
  • Biological Unit Coordinates (2v3d.pdb2.gz) 92 Kb
  • LPC: Ligand-Protein Contacts for 2V3D
  • CSU: Contacts of Structural Units for 2V3D
  • Likely Quarternary Molecular Structure file(s) for 2V3D
  • Structure Factors (562 Kb)
  • Retrieve 2V3D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2V3D from S2C, [Save to disk]
  • Re-refined 2v3d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2V3D 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 2V3D
  • 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 2V3D, from MSDmotif at EBI
  • Fold representative 2v3d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2v3d] [2v3d_A] [2v3d_B]
  • SWISS-PROT database: [P04062]
  • Domain organization of [GLCM_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2V3D with the sequences similar proteins can be viewed for 2V3D's classification [GLCM_HUMAN] 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_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2V3D
  • Community annotation for 2V3D 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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