2WCG	Hydrolase	date	Mar 12, 2009
title	X-Ray Structure Of Acid-Beta-Glucosidase With N-Octyl( Cyclic Guanidine)-Nojirimycin In The Active Site
authors	B.Brumshtein, M.Aguilar, M.I.Garcia-Moreno, C.O.Mellet, J.M.Garcia-Fernandez, I.Silman, Y.Shaaltiel, D.Aviezer, J.L.Sussman, A.H.Futerman
compound		source
Molecule: Glucosylceramidase Chain: A, B Fragment: Residues 40-536 Ec: 3.2.1.45 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Daucus Carota Expression_system_taxid: 4039
symmetry	Space Group: P 1 21 1	R_factor 0.135 R_Free 0.194
crystal cell	length a length b length c angle alpha angle beta angle gamma 68.311 96.827 83.234 90.00 104.34 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	CL, FU4, MAN, MT5, NAG, SO4	enzyme	Hydrolase E.C.3.2.1.45 BRENDA
Gene Ontology	Chain Function Process Component A, 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	6-Amino-6-deoxy-5,6-di-N-(N'-octyliminomethylidene)nojirimycin: synthesis, biological evaluation, and crystal structure in complex with acid beta-glucosidase., Brumshtein B, Aguilar-Moncayo M, Garcia-Moreno MI, Ortiz Mellet C, Garcia Fernandez JM, Silman I, Shaaltiel Y, Aviezer D, Sussman JL, Futerman AH, Chembiochem. 2009 Jun 15;10(9):1480-5. PMID:19437524

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk] Biological Unit Coordinates (2wcg.pdb1.gz) 89 Kb Biological Unit Coordinates (2wcg.pdb2.gz) 89 Kb LPC: Ligand-Protein Contacts for 2WCG CSU: Contacts of Structural Units for 2WCG Structure Factors (642 Kb) Retrieve 2WCG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2WCG from S2C, [Save to disk] Re-refined 2wcg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2WCG 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 2WCG

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 2WCG, from MSDmotif at EBI Fold representative 2wcg from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2wcg_A] [2wcg_B] SWISS-PROT database: [P04062] Domain organization of [GLCM_HUMAN] by SWISSPFAM Alignments of the sequence of 2WCG with the sequences similar proteins can be viewed for 2WCG'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 2WCG

Community annotation for 2WCG at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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