OCA Atlas for 2WKL

2WKL

Hydrolase

date

Jun 15, 2009

title

Velaglucerase Alfa

authors

B.Brumshtein, P.Salinas, B.Peterson, V.Chan, I.Silman, J.L.Sussman, P.J.Savickas, G.S.Robinson, A.H.Futerman

compound

source

Molecule: Glucosylceramidase
Chain: A, B
Synonym: Beta-Glucocerebrosidase, Acid Beta-Glucosidase, D-Glucosyl-N-Acylsphingosine Glucohydrolase, Alglucerase, Imiglucerase;
Ec: 3.2.1.45
Other_details: Glycosylation On Asn19 Chain A, Asn146 Chain A And On Asn19 Chain B

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

symmetry

Space Group: C 2 2 21

R_factor

0.17293

R_Free

0.23392

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
109.371	285.552	91.693	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.70 Å

ligand

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

Characterization of Gene-activated Human Acid-{beta}-Glucosidase: Crystal Structure, Glycan Composition and Internalization into Macrophages., Brumshtein B, Salinas P, Peterson B, Chan V, Silman I, Sussman JL, Savickas PJ, Robinson GS, Futerman AH, Glycobiology. 2009 Sep 9. PMID:19741058

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (173 Kb) [Save to disk]

Biological Unit Coordinates (2wkl.pdb1.gz) 84 Kb

Biological Unit Coordinates (2wkl.pdb2.gz) 85 Kb

LPC: Ligand-Protein Contacts for 2WKL

CSU: Contacts of Structural Units for 2WKL

Structure Factors (346 Kb)

Retrieve 2WKL in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2WKL from S2C, [Save to disk]

Re-refined 2wkl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2WKL 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 2WKL

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 2WKL, from MSDmotif at EBI

Fold representative 2wkl from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2wkl_A] [2wkl_B]

SWISS-PROT database: [P04062]

Domain organization of [GLCM_HUMAN] by SWISSPFAM

Alignments of the sequence of 2WKL with the sequences similar proteins can be viewed for 2WKL'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 2WKL

Community annotation for 2WKL at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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