4DGI Structure of POM1 FAB fragment complexed with human PrPc Fragment 120-230 date 2012-01-26
authors Baral, P.K., Wieland, B., Swayampakula, M., James, M.N.
compound source
symmetry
R_factor
R_Free 0.2893
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.40
ligand NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural studies on the folded domain of the human prion protein bound to the Fab fragment of the antibody POM1., Baral PK, Wieland B, Swayampakula M, Polymenidou M, Rahman MH, Kav NN, Aguzzi A, James MN, Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1501-12. doi:, 10.1107/S0907444912037328. Epub 2012 Oct 18. PMID:23090399
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (4dgi.pdb1.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 4DGI
  • CSU: Contacts of Structural Units for 4DGI
  • Structure Factors (405 Kb)
  • Retrieve 4DGI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DGI from S2C, [Save to disk]
  • Re-refined 4dgi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DGI 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 4DGI
  • 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 4DGI, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dgi_H] [4dgi_A] [4dgi] [4dgi_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DGI: [IG_like] [IGv] [PRP ] by SMART
    • Other resources with information on 4DGI
  • Community annotation for 4DGI at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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