4MD4 Immune Receptor date 2013-08-22
authors Scally, S.W., Rossjohn, J.
compound source
symmetry
R_factor
R_Free 0.2091
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.95
ligand CIR, EDO, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceA molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis., Scally SW, Petersen J, Law SC, Dudek NL, Nel HJ, Loh KL, Wijeyewickrema LC, Eckle SB, van Heemst J, Pike RN, McCluskey J, Toes RE, La Gruta NL, Purcell AW, Reid HH, Thomas R, Rossjohn J, J Exp Med. 2013 Nov 18;210(12):2569-82. doi: 10.1084/jem.20131241. Epub 2013 Nov , 4. PMID:24190431
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (4md4.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 4MD4
  • CSU: Contacts of Structural Units for 4MD4
  • Structure Factors (2028 Kb)
  • Retrieve 4MD4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4MD4 from S2C, [Save to disk]
  • Re-refined 4md4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4MD4 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 4MD4
  • 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 4MD4, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4md4] [4md4_A] [4md4_C] [4md4_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4MD4: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
    • Other resources with information on 4MD4
  • Community annotation for 4MD4 at PDBWiki (http://pdbwiki.org)

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