3GXM	Hydrolase	date	Apr 02, 2009
title	Crystal Structure Of Acid-Beta-Glucosidase At Ph 4.5, Phosph Crystallization Condition
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 Expression_system_taxid: 10029
symmetry	Space Group: P 1 21 1	R_factor 0.220 R_Free 0.276
crystal cell	length a length b length c angle alpha angle beta angle gamma 110.505 91.779 152.751 90.00 111.24 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	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	Effects 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] (350 Kb) [Save to disk] Biological Unit Coordinates (3gxm.pdb1.gz) 342 Kb Biological Unit Coordinates (3gxm.pdb2.gz) 341 Kb Biological Unit Coordinates (3gxm.pdb3.gz) 174 Kb Biological Unit Coordinates (3gxm.pdb4.gz) 174 Kb LPC: Ligand-Protein Contacts for 3GXM CSU: Contacts of Structural Units for 3GXM Likely Quarternary Molecular Structure file(s) for 3GXM Structure Factors (2222 Kb) Retrieve 3GXM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GXM from S2C, [Save to disk] Re-refined 3gxm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GXM 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 3GXM

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 3GXM, from MSDmotif at EBI Fold representative 3gxm from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gxm_A] [3gxm_B] [3gxm_C] [3gxm_D] SWISS-PROT database: [P04062] Domain organization of [GLCM_HUMAN] by SWISSPFAM Alignments of the sequence of 3GXM with the sequences similar proteins can be viewed for 3GXM'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 3GXM

Community annotation for 3GXM at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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