At 25A the only discerning feature between Fabs is probably the elbow angle and a rigid body fit might be enough to discriminate between those.
http://www.ruppweb.org/cvs/br/Stanfield_2006_JMB_antibody_elbow_angle.pdf Best br On Mon, Jul 27, 2020, 21:10 Roversi, Pietro (Dr.) <pr...@leicester.ac.uk> wrote: > Dear all, > > I am fitting a 25 Å negative stain EM map of a protein in complex with its > FAb. I have restraints on the protein region the FAb recognises (from > ELISAs on truncated versions of the protein) but I do not have the sequence > of the FAb. > > I have a model for the protein and I picked a FAb from the PDB to be a > representative FAb model which I believe is good enough to fit a 25 Å > negative stain EM map. By "good enough" I mean: this model would answer the > question: " Can I fit this map with the protein and a FAb model and would > the relative FAb:protein arrangement satisfy the known restraints on the > FAb epitope?" > > A PDB search with "unknown sequence" returns 17 entries: > > 1IVI,1TNV,1HR3,1QTJ,4CAT,2PGK,1PYK,1KGA,4GL8,1HKG,2YHX,1GRH,3LDH,4I79,1SNB,6IJ1,3CKM > > What is your experience with depositing into the PDB structures of > proteins of unknown sequence? > > And as a user, would you accept an entry with a FAb as poly-Ala or Calphas > only and poly-UNK? > > Thank you for any feedback you'll be able to let me have, > > with best wishes, > > Pietro > > > > > > > > > > Pietro Roversi > > Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/ > > LISCB Wellcome Trust ISSF Fellow > > <https://bit.ly/2I4Wm5Z> > https://le.ac.uk/liscb/research-groups/pietro-roversi > > > Leicester Institute of Structural and Chemical Biology > Department of Molecular and Cell Biology, University of Leicester > Henry Wellcome Building > Lancaster Road, Leicester, LE1 7HB > England, United Kingdom > > Skype: roversipietro > Mobile phone +44 (0) 7927952047 > Tel. +44 (0)116 2297237 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
