2YD6 Hydrolase date Mar 17, 2011
title Crystal Structure Of The N-Terminal Ig1-2 Module Of Human Re Protein Tyrosine Phosphatase Delta
authors C.H.Coles, Y.Shen, A.P.Tenney, C.Siebold, G.C.Sutton, W.Lu, J.T.Ga E.Y.Jones, J.G.Flanagan, A.R.Aricescu
compound source
Molecule: Ptprd Protein
Chain: A
Fragment: Ig1-2, Residues 21-220
Synonym: Rptpd, Receptor Protein Tyrosine Phosphatase Delta
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
Expression_system_vector_type: Plasmid
Expression_system_vector: Phlsec
symmetry Space Group: P 32 2 1
R_factor 0.141 R_Free 0.171
length a length b length c angle alpha angle beta angle gamma
48.710 48.710 145.910 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.35 Å
ligand CL, FLC enzyme Hydrolase E.C. BRENDA
note 2YD6 is a representative structure
Primary referenceProteoglycan-Specific Molecular Switch for RPTP{sigma} Clustering and Neuronal Extension., Coles CH, Shen Y, Tenney AP, Siebold C, Sutton GC, Lu W, Gallagher JT, Jones EY, Flanagan JG, Aricescu AR, Science. 2011 Mar 31. PMID:21454754
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (2yd6.pdb1.gz) 156 Kb
  • LPC: Ligand-Protein Contacts for 2YD6
  • CSU: Contacts of Structural Units for 2YD6
  • Structure Factors (529 Kb)
  • Retrieve 2YD6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YD6 from S2C, [Save to disk]
  • Re-refined 2yd6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YD6 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 2YD6
  • 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 2YD6, from MSDmotif at EBI
  • Fold representative 2yd6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yd6] [2yd6_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YD6: [IGc2 ] by SMART
  • Other resources with information on 2YD6
  • Community annotation for 2YD6 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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