The lazy mans way - submit it to Modelcraft with the 11 peptide sequence and the rest of the structure as the "fixed model". Eleanor
On Fri, 28 Feb 2025 at 08:53, Rigden, Dan <drig...@liverpool.ac.uk> wrote: > Dear Manjula > > You can use AlphaFold 3 (https://alphafoldserver.com/) to predict > structures of the phosphopeptide, and the structure of the > protein-phosphopeptide complex. These might give you useful starting > hypotheses that have some (partial) support in the density. The complex > prediction will be more reliable if a) something similar has been seen in > the PDB and/or b) if the phosphopeptide is, or is derived from/based on, a > sequence that naturally interacts with the protein receptor. You would, of > course, use the pLDDT and PAE plots and the p(I)TM scores to help judge how > much confidence you should have in the predictions ( > https://alphafoldserver.com/guides#section-3:-interpreting-results-from-alphafold-server > ). > > Best wishes > Dan > > Prof Daniel Rigden (He/Him) > Department of Biochemistry, Cell and Systems Biology > Institute of Systems, Molecular and Integrative Biology > Room 101, Biosciences Building > University of Liverpool > Crown St., Liverpool, L69 7ZB > > (+44) 151 795 4467 > > www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/daniel-rigden/ > Scholar Google > <https://scholar.google.co.uk/citations?user=8l7rbMIAAAAJ&hl=en> > @danielrigden.bsky.social > <https://bsky.app/profile/danielrigden.bsky.social> > > > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Manjula > Ramu <manjula....@gmail.com> > *Sent:* 27 February 2025 21:09 > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* [ccp4bb] unable to fit the 11-amino-acid peptide > > > Caution: This email originated from outside of the University. Do not > click links or open attachments unless you recognise the source of this > email and know the content is safe. Check sender address, hover over URLs > and don't open suspicious email attachments. > Dear all, > > I recently solved a complex structure of a protein with an 11-amino-acid > phosphopeptide at 2.58 Å resolution. The asymmetric unit contains two > protein chains, and the difference map shows positive green density (Fo-Fc > positive difference density) for the peptide. However, the density is not > well-defined, making manual fitting of the peptide challenging. > > I have two key questions: > > 1. *How can I generate a 3D model of the 11-residue phosphopeptide?* > 2. *What options are available for fitting the peptide into the > electron density?* > > I would greatly appreciate any guidance or suggestions to help complete my > structure. I have attached the png file from the coot. > > ---------------------------------------------------- > > Thanks and Regards, > > *Manjula * > > > > > > <https://www.nimhans.kar.nic.in/> > > ------------------------------ > > 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 > ######################################################################## 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/
