4P4K Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between allergic hypersensitivity and auto immunity date
authors Clayton, G.M., Crawford, F., Kappler, J.W.
compound source
symmetry
R_factor
R_Free 0.2518
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand 0BE, NA, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


F, B


Primary referenceStructural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity., Clayton GM, Wang Y, Crawford F, Novikov A, Wimberly BT, Kieft JS, Falta MT, Bowerman NA, Marrack P, Fontenot AP, Dai S, Kappler JW, Cell. 2014 Jul 3;158(1):132-42. doi: 10.1016/j.cell.2014.04.048. PMID:24995984
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (272 Kb) [Save to disk]
  • Biological Unit Coordinates (4p4k.pdb1.gz) 135 Kb
  • Biological Unit Coordinates (4p4k.pdb2.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 4P4K
  • CSU: Contacts of Structural Units for 4P4K
  • Structure Factors (448 Kb)
  • Retrieve 4P4K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4P4K from S2C, [Save to disk]
  • Re-refined 4p4k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4P4K 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 4P4K
  • 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 4P4K, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4p4k_B] [4p4k_H] [4p4k_D] [4p4k_E] [4p4k_A] [4p4k_F] [4p4k] [4p4k_G] [4p4k_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4P4K: [IG] [IG_like] [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
    • Other resources with information on 4P4K
  • Community annotation for 4P4K at PDBWiki (http://pdbwiki.org)

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