3RIL 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
Synonym: Acid Beta-Glucosidase, Alglucerase, Beta-Glucocere D-Glucosyl-N-Acylsphingosine Glucohydrolase, Imiglucerase;
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 0.171 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
109.217 91.425 152.659 90.00 110.95 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 3RK, NAG, SO4 BindingDB enzyme Hydrolase E.C. BRENDA
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] (354 Kb) [Save to disk]
  • Biological Unit Coordinates (3ril.pdb1.gz) 345 Kb
  • Biological Unit Coordinates (3ril.pdb2.gz) 345 Kb
  • Biological Unit Coordinates (3ril.pdb3.gz) 345 Kb
  • Biological Unit Coordinates (3ril.pdb4.gz) 345 Kb
  • Biological Unit Coordinates (3ril.pdb5.gz) 345 Kb
  • LPC: Ligand-Protein Contacts for 3RIL
  • CSU: Contacts of Structural Units for 3RIL
  • Structure Factors (1701 Kb)
  • Retrieve 3RIL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RIL from S2C, [Save to disk]
  • Re-refined 3ril structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RIL 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 3RIL
  • 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 3RIL, from MSDmotif at EBI
  • Fold representative 3ril from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ril] [3ril_C] [3ril_D] [3ril_B] [3ril_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3RIL with the sequences similar proteins can be viewed for 3RIL'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 3RIL
  • Community annotation for 3RIL at PDBWiki (http://pdbwiki.org)
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