4OD2 Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5 date 2014-01-09
authors Hymowitz, S.G., Compaan, D.
compound source
symmetry
R_factor
R_Free 0.30463
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.20
Gene
Ontology
ChainFunctionProcessComponent
S


Primary referenceStructural and functional analysis of the interaction between the agonistic monoclonal antibody Apomab and the proapoptotic receptor DR5., Adams C, Totpal K, Lawrence D, Marsters S, Pitti R, Yee S, Ross S, Deforge L, Koeppen H, Sagolla M, Compaan D, Lowman H, Hymowitz S, Ashkenazi A, Cell Death Differ. 2008 Apr;15(4):751-61. doi: 10.1038/sj.cdd.4402306. Epub 2008 , Jan 25. PMID:18219321
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (173 Kb) [Save to disk]
  • Biological Unit Coordinates (4od2.pdb1.gz) 166 Kb
  • CSU: Contacts of Structural Units for 4OD2
  • Structure Factors (208 Kb)
  • Retrieve 4OD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4OD2 from S2C, [Save to disk]
  • Re-refined 4od2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4OD2 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 4OD2
  • 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 4OD2, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4od2] [4od2_A] [4od2_S] [4od2_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4OD2: [IG_like] [IGv] [TNFR ] by SMART
    • Other resources with information on 4OD2
  • Community annotation for 4OD2 at PDBWiki (http://pdbwiki.org)

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