Antibody PDB Acknowledgements

Note for people downloading the Chime presentation: the larger PDB files are gzipped, and must be decompressed (gzip -d filename) before they can be viewed in RasMol. Therefore you may prefer to download the uncompressed files directly from the links below.

Tetrapeptide. Residues 4-7 of the peptide chain B were excerpted by manual editing from 1ROG.PDB by D. Rognan, L. Scapozza, G. Folkers, and A. Daser, July 1994, a complex between the MHC molecule HLA-B27 and a nonapeptide. This was chosen because it was theoretically modeled and included some (but not all!) hydrogens. ( Madden/Wiley Cell 1994).
Immunoglobulin domain. The light chain constant domain (chain L, residues 105-214) was excerpted by manual editing from 1FDL.PDB (see below).
Fab:lysozyme complex. This is 1FDL.PDB, mouse monoclonal IgG1 D1.3 with hen egg white lysozyme, by T. O. Fischman and R. J. Poljak, August 1990 ( Fischmann/Poljak, JBC, 1991).
F(ab')₂. This is BIO2IG2.PDB, in which the second Fab' arm of 2IG2.PDB has been generated by a symmetry operation. This human IgG1 came from myeloma patient KOL, and the structure was deposited by M. Marquart and R. Huber, July 1989. ( Marquart/Palm, JMB 1980; M. Marquart and J. Deisenhofer, The three-dimensional structure of antibodies, Immunol. Today, 3:160, 1982).
Intact IgG1 with carbohydrate. This PDB file was created and kindly provided by Eduardo A. Padlan, who combined the Fab' from 2IG2.PDB (see above) with the Fc from 1FC2.PDB, and modeled in the hinge region ( Padlan, MI 1994). This PDB file for intact IgG1 can be downloaded from the RasMol Home Page under Exclusive Molecules. If you put it on a web site, please cite the above Padlan reference.