4B53 Immune System date Aug 02, 2012
title Crystal Structure Of The Isolated Igg4 Ch3 Domain
authors A.M.Davies, T.Rispens, T.H.Den Bleker, J.M.Mcdonnell, H.J.Gould, R.C.Aalberse, B.J.Sutton
compound source
Molecule: Ig Gamma-4 Chain C Region
Chain: A, B
Fragment: Ch3 Domain, Residues 222-327
Synonym: Human Igg4
Engineered: Yes
Other_details: N Terminal Glutamine 342 Is Modified To Pyro
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293f
symmetry Space Group: P 43 2 2
R_factor 0.183 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.090 57.090 138.436 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand ACT, EDO, PCA, PEG, TRS enzyme
Primary referenceCrystal structure of the human IgG4 C(H)3 dimer reveals the role of Arg409 in the mechanism of Fab-arm exchange., Davies AM, Rispens T, den Bleker TH, McDonnell JM, Gould HJ, Aalberse RC, Sutton BJ, Mol Immunol. 2012 Nov 16;54(1):1-7. doi: 10.1016/j.molimm.2012.10.029. PMID:23164605
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (4b53.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 4B53
  • CSU: Contacts of Structural Units for 4B53
  • Structure Factors (154 Kb)
  • Retrieve 4B53 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B53 from S2C, [Save to disk]
  • Re-refined 4b53 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4B53 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 4B53
  • 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 4B53, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b53_A] [4b53_B] [4b53]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4B53: [IGc1 ] by SMART
  • Other resources with information on 4B53
  • Community annotation for 4B53 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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