2NT0	Hydrolase	date	Nov 06, 2006
title	Acid-Beta-Glucosidase Low Ph, Glycerol Bound
authors	R.L.Lieberman, G.A.Petsko, D.Ringe
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 Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_organ: Ovary
symmetry	Space Group: P 1 21 1	R_factor 0.179 R_Free 0.215
crystal cell	length a length b length c angle alpha angle beta angle gamma 107.941 91.759 152.810 90.00 110.96 90.00
method	X-Ray Diffraction	resolution	1.79 Å
ligand	GOL, NAG, SO4	enzyme	Hydrolase E.C.3.2.1.45 BRENDA
note	2NT0 is a representative structure
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	Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease., Lieberman RL, Wustman BA, Huertas P, Powe AC Jr, Pine CW, Khanna R, Schlossmacher MG, Ringe D, Petsko GA, Nat Chem Biol. 2007 Feb;3(2):101-7. Epub 2006 Dec 24. PMID:17187079

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (362 Kb) [Save to disk] Biological Unit Coordinates (2nt0.pdb1.gz) 93 Kb Biological Unit Coordinates (2nt0.pdb2.gz) 94 Kb Biological Unit Coordinates (2nt0.pdb3.gz) 93 Kb Biological Unit Coordinates (2nt0.pdb4.gz) 94 Kb LPC: Ligand-Protein Contacts for 2NT0 CSU: Contacts of Structural Units for 2NT0 Structure Factors (1880 Kb) Retrieve 2NT0 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2NT0 from S2C, [Save to disk] Re-refined 2nt0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2NT0 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 2NT0

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 2NT0, from MSDmotif at EBI Fold representative 2nt0 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2nt0_A] [2nt0_B] [2nt0_C] [2nt0_D] SWISS-PROT database: [P04062] Domain organization of [GLCM_HUMAN] by SWISSPFAM Alignments of the sequence of 2NT0 with the sequences similar proteins can be viewed for 2NT0'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 2NT0

Community annotation for 2NT0 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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