2XWD Hydrolase date Nov 01, 2010
title X-Ray Structure Of Acid-Beta-Glucosidase With 5n,6o-(N'-(N- Octyl)Imino)Nojirimycin In The Active Site
authors B.Brumshtein, M.Aguilar-Moncayo, J.M.Benito, C.Ortiz Mellet, J.M.Garcia Fernandez, I.Silman, Y.Shaaltiel, J.L.Sussman, A.H.F
compound source
Molecule: Glucosylceramidase
Chain: A, B
Synonym: Acid-Beta-Glucosidase, Alglucerase, Beta-Glucocerebrosidase, D-Glucosyl-N-Acylsphingosine Glucohydrolase, Imiglucerase;
Ec: 3.2.1.45
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Daucus Carota
Expression_system_common: Carrot
Expression_system_taxid: 4039
symmetry Space Group: P 1 21 1
R_factor 0.15003 R_Free 0.21893
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.036 96.617 83.164 90.00 103.69 90.00
method X-Ray Diffractionresolution 2.66 Å
ligand BMA, FUC, LGS, MAN, NAG, SO4 enzyme Hydrolase E.C.3.2.1.45 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • negative regulation of inter...

  • Primary referenceCyclodextrin-mediated crystallization of acid beta-glucosidase in complex with amphiphilic bicyclic nojirimycin analogues., Brumshtein B, Aguilar-Moncayo M, Benito JM, Garcia Fernandez JM, Silman I, Shaaltiel Y, Aviezer D, Sussman JL, Futerman AH, Ortiz Mellet C, Org Biomol Chem. 2011 Jun 7;9(11):4160-7. Epub 2011 Apr 11. PMID:21483943
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (172 Kb) [Save to disk]
  • Biological Unit Coordinates (2xwd.pdb1.gz) 84 Kb
  • Biological Unit Coordinates (2xwd.pdb2.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 2XWD
  • CSU: Contacts of Structural Units for 2XWD
  • Structure Factors (328 Kb)
  • Retrieve 2XWD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XWD from S2C, [Save to disk]
  • Re-refined 2xwd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XWD 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 2XWD
  • 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 2XWD, from MSDmotif at EBI
  • Fold representative 2xwd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xwd_A] [2xwd_B] [2xwd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 2XWD with the sequences similar proteins can be viewed for 2XWD's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2XWD
  • Community annotation for 2XWD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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