2YD3 Hydrolase date Mar 17, 2011
title Crystal Structure Of The N-Terminal Ig1-2 Module Of Human Receptor Protein Tyrosine Phosphatase Sigma
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: Receptor-Type Tyrosine-Protein Phosphatase S
Chain: A
Fragment: Ig1-2, Residues 30-228
Synonym: Protein Tyrosine Phosphatase Sigma, R-Ptp-S, Recep Tyrosine-Protein Phosphatase Sigma, R-Ptp-Sigma, Rptps;
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: I 41 2 2
R_factor 0.2007 R_Free 0.2350
length a length b length c angle alpha angle beta angle gamma
104.218 104.218 94.850 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CL, NA enzyme Hydrolase E.C. BRENDA
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] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (2yd3.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 2YD3
  • CSU: Contacts of Structural Units for 2YD3
  • Structure Factors (91 Kb)
  • Retrieve 2YD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YD3 from S2C, [Save to disk]
  • Re-refined 2yd3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YD3 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 2YD3
  • 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 2YD3, from MSDmotif at EBI
  • Fold representative 2yd3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yd3_A] [2yd3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YD3: [IGc2 ] by SMART
  • Other resources with information on 2YD3
  • Community annotation for 2YD3 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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