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, O-Glcnacase, Hexosaminidase B, N-Acetyl-Beta-Glucosaminida
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-Interacting Protein 1, Tgf-Beta-Activated Kinase 1-Bindi Protein 1, Tak1-Binding Protein 1;
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 0.20007 R_Free 0.23846
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 Diffractionresolution 2.55 Å
ligand CD, NAG enzyme Hydrolase E.C.3.2.1.169 BRENDA
Primary referenceSynergy 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] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (2yds.pdb1.gz) 97 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
  • 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 2YDS, from MSDmotif at EBI
  • Fold representative 2yds from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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