3W9Y Peptide Binding Protein date Apr 18, 2013
title Crystal Structure Of The Human Dlg1 Guanylate Kinase Domain
authors S.Mori, Y.Tezuka, A.Arakawa, N.Handa, M.Shirouzu, T.Akiyama, S.Yok
compound source
Molecule: Disks Large Homolog 1
Chain: A
Fragment: Guanylate Kinase Domain, Unp Residues 734-926
Synonym: Synapse-Associated Protein 97, Sap-97, Sap97, Hdlg
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dlg1
Expression_system: Cell-Free Synthesis
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcr2.1-Topo
symmetry Space Group: P 65 2 2
R_factor 0.209 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.535 65.535 180.563 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand MSE enzyme
Primary referenceCrystal structure of the guanylate kinase domain from discs large homolog 1 (DLG1/SAP97)., Mori S, Tezuka Y, Arakawa A, Handa N, Shirouzu M, Akiyama T, Yokoyama S, Biochem Biophys Res Commun. 2013 Jun 7;435(3):334-8. doi:, 10.1016/j.bbrc.2013.04.056. Epub 2013 Apr 25. PMID:23624197
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (3w9y.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 3W9Y
  • CSU: Contacts of Structural Units for 3W9Y
  • Structure Factors (254 Kb)
  • Retrieve 3W9Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3W9Y from S2C, [Save to disk]
  • Re-refined 3w9y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3W9Y 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 3W9Y
  • 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 3W9Y, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3w9y_A] [3w9y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3W9Y: [GuKc ] by SMART
    • Other resources with information on 3W9Y
  • Community annotation for 3W9Y at PDBWiki (http://pdbwiki.org)

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