2YDS	Hydrolase Peptide	date	Mar 24, 2011
title	Cpoga D298n In Complex With Tab1-Derived O-Glcnac Peptide
authors	M.Schimpl, V.S.Borodkin, L.J.Gray, D.M.F.Van Aalten
compound		source
Molecule: O-Glcnacase Nagj Chain: A Fragment: Residues 31-618 Synonym: Beta-N-Acetylhexosaminidase, Beta-Hexosaminidase, Glcnacase, Hexosaminidase B, N-Acetyl-Beta-Glucosaminidase; Ec: 3.2.1.169 Engineered: Yes Mutation: Yes Other_details: Cpnagj		Organism_scientific: Clostridium Perfringens Organism_taxid: 1502 Atcc: 13124 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex6p-1
Molecule: Tgf-Beta-Activated Kinase 1 And Map3k7-Binding Pr Chain: T Fragment: Residues 392-398 Synonym: Mitogen-Activated Protein Kinase Kinase Kinase 7-I Protein 1, Tgf-Beta-Activated Kinase 1-Binding Protein 1, T Binding Protein 1; Engineered: Yes Other_details: O-Glcnac Glycosylation On S395		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: P 61	R_factor 0.200 R_Free 0.238
crystal cell	length a length b length c angle alpha angle beta angle gamma 118.090 118.090 148.260 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.55 Å
ligand	CD, NAG	enzyme	Hydrolase E.C.3.2.1.169 BRENDA
Primary reference	Synergy of Peptide and Sugar in O-GlcNAcase Substrate Recognition., Schimpl M, Borodkin VS, Gray LJ, van Aalten DM, Chem Biol. 2012 Feb 24;19(2):173-8. PMID:22365600

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk] Biological Unit Coordinates (2yds.pdb1.gz) 95 Kb LPC: Ligand-Protein Contacts for 2YDS CSU: Contacts of Structural Units for 2YDS Structure Factors (512 Kb) Retrieve 2YDS in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2YDS from S2C, [Save to disk] Re-refined 2yds structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2YDS 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.

Visual 3D analysis of 2YDS

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 3D motif for 2YDS, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2yds_A] [2yds] [2yds_T] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 2YDS

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

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