3RIK Hydrolase Hydrolase Inhibitor date Apr 13, 2011
title The Acid Beta-Glucosidase Active Site Exhibits Plasticity In 3,4,5,6-Tetrahydroxyazepane-Based Inhibitors: Implications Pharmacological Chaperone Design For Gaucher Disease
authors S.D.Orwig, R.L.Lieberman
compound source
Molecule: Glucosylceramidase
Chain: A, B, C, D
Fragment: Residues 40-536
Synonym: Acid Beta-Glucosidase, Alglucerase, Beta-Glucocere D-Glucosyl-N-Acylsphingosine Glucohydrolase, 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
Expression_system_taxid: 10029
symmetry Space Group: P 1 21 1
R_factor 0.162 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.980 91.553 152.213 90.00 110.70 90.00
method X-Ray Diffractionresolution 2.48 Å
ligand 3RI, NAG, SO4 enzyme Hydrolase E.C.3.2.1.45 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • negative regulation of inter...

  • Primary referenceBinding of 3,4,5,6-tetrahydroxyazepanes to the acid-beta-glucosidase active site: implications for pharmacological chaperone design for Gaucher disease., Orwig SD, Tan YL, Grimster NP, Yu Z, Powers ET, Kelly JW, Lieberman RL, Biochemistry. 2011 Dec 13;50(49):10647-57. Epub 2011 Nov 14. PMID:22047104
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (348 Kb) [Save to disk]
  • Biological Unit Coordinates (3rik.pdb1.gz) 90 Kb
  • Biological Unit Coordinates (3rik.pdb2.gz) 90 Kb
  • Biological Unit Coordinates (3rik.pdb3.gz) 90 Kb
  • Biological Unit Coordinates (3rik.pdb4.gz) 89 Kb
  • Biological Unit Coordinates (3rik.pdb5.gz) 340 Kb
  • LPC: Ligand-Protein Contacts for 3RIK
  • CSU: Contacts of Structural Units for 3RIK
  • Structure Factors (1489 Kb)
  • Retrieve 3RIK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RIK from S2C, [Save to disk]
  • Re-refined 3rik structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RIK 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 3RIK
  • 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 3RIK, from MSDmotif at EBI
  • Fold representative 3rik from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rik_A] [3rik] [3rik_D] [3rik_B] [3rik_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RIK
  • Community annotation for 3RIK at PDBWiki (http://pdbwiki.org)
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