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 Diffraction	resolution	2.48 Å
ligand	3RI, NAG, SO4	enzyme	Hydrolase E.C.3.2.1.45 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B glucosylceramidase activity receptor binding hydrolase activity hydrolase activity, acting o... lipid metabolic process sphingolipid metabolic proce... glucosylceramide catabolic p... glycosphingolipid metabolic ... metabolic process cell death termination of signal transd... negative regulation of inter... positive regulation of prote... negative regulation of MAP k... small molecule metabolic pro... sphingosine biosynthetic pro... ceramide biosynthetic proces... negative regulation of infla... cellular response to tumor n... lysosome lysosomal membrane membrane lysosomal lumen
Primary reference	Binding 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_B] [3rik_C] [3rik_D] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3RIK with the sequences similar proteins can be viewed for 3RIK'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 3RIK

Community annotation for 3RIK at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2010 Bioinformatics Unit Weizmann Institute of Science

---