3GXD Hydrolase date Apr 02, 2009
title Crystal Structure Of Apo Acid-Beta-Glucosidase Ph 4.5
authors R.L.Lieberman
compound source
Molecule: Glucosylceramidase
Chain: A, B, C, D
Synonym: Beta-Glucocerebrosidase, Acid Beta-Glucosidase, D- N-Acylsphingosine Glucohydrolase, Alglucerase, Imiglucerase
Ec: 3.2.1.45
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gba, Gc, Gluc
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
symmetry Space Group: P 1 21 1
R_factor 0.204 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.442 91.703 152.491 90.00 111.04 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand NAG, PO4 enzyme Hydrolase E.C.3.2.1.45 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • negative regulation of inter...

  • Primary referenceEffects of pH and Iminosugar Pharmacological Chaperones on Lysosomal Glycosidase Structure and Stability., Lieberman RL, D'aquino JA, Ringe D, Petsko GA, Biochemistry. 2009 May 1. PMID:19374450
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (336 Kb) [Save to disk]
  • Biological Unit Coordinates (3gxd.pdb1.gz) 328 Kb
  • LPC: Ligand-Protein Contacts for 3GXD
  • CSU: Contacts of Structural Units for 3GXD
  • Likely Quarternary Molecular Structure file(s) for 3GXD
  • Structure Factors (1345 Kb)
  • Retrieve 3GXD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GXD from S2C, [Save to disk]
  • Re-refined 3gxd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GXD 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 3GXD
  • 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 3GXD, from MSDmotif at EBI
  • Fold representative 3gxd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gxd_C] [3gxd_A] [3gxd_D] [3gxd] [3gxd_B]
  • SWISS-PROT database: [P04062]
  • Domain organization of [GLCM_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 3GXD with the sequences similar proteins can be viewed for 3GXD'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 3GXD
  • Community annotation for 3GXD 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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