This is not the “Lazy Man’s Way”, this is The Way. Especially when you have such nice electron density. Although I would attempt to correct as many errors for side chain rotamers in the protein structure first.
Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) On Feb 28, 2025, at 4:57 AM, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: External Mail This email originated from outside of UT Southwestern. Please be cautious. <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/MznTZTSvDXGV0Co!W_xDF9j-YRUzYxOlhd6ZgirNyJqsGDA7zswLqHXhngRHM02zcZLiMH4WD1tIPGwFT2uVXCSonY-VvvTkSCHMcBGP_h_m2ouoe0n-YPCLApl7qyqUdxC5IxvvCowk2ryavIqjNcSx$> Report Suspicious The lazy mans way - submit it to Modelcraft with the 11 peptide sequence and the rest of the structure as the "fixed model". Eleanor On Fri, 28 Feb 2025 at 08:53, Rigden, Dan <drig...@liverpool.ac.uk<mailto:drig...@liverpool.ac.uk>> wrote: Dear Manjula You can use AlphaFold 3 (https://alphafoldserver.com/<https://urldefense.com/v3/__https://alphafoldserver.com/__;!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcGHUMquw$>) 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<https://urldefense.com/v3/__https://alphafoldserver.com/guides*section-3:-interpreting-results-from-alphafold-server__;Iw!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcT6YlPyY$>). Best wishes Dan Prof Daniel Rigden (He/Him) Department of Biochemistry, Cell and Systems Biology Institute of Systems, Molecular and Integrative Biology Room 101, Biosciences Building University of Liverpool Crown St., Liverpool, L69 7ZB (+44) 151 795 4467 www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/daniel-rigden/<https://urldefense.com/v3/__http://www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/daniel-rigden/__;!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcXnuCgrg$> Scholar Google<https://urldefense.com/v3/__https://scholar.google.co.uk/citations?user=8l7rbMIAAAAJ&hl=en__;!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcWwJZ5v0$> @danielrigden.bsky.social<https://urldefense.com/v3/__https://bsky.app/profile/danielrigden.bsky.social__;!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcUEeP-3I$> <Outlook-01iwlcgj.jpg> ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Manjula Ramu <manjula....@gmail.com<mailto:manjula....@gmail.com>> Sent: 27 February 2025 21:09 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto: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://urldefense.com/v3/__https://www.nimhans.kar.nic.in/__;!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcISLHppU$> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcAn52vfs$> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcAn52vfs$> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!FVkL16HlFtkFbEVYoOGwb9QyVoqe0pEgfbobZQXYp8863QrinxZheHHw5PIAOhHw_bY-Hjg8iKlKUXg314NmaLwGiz9m5kdqQU90I5YcAn52vfs$> ________________________________ UT Southwestern Medical Center The future of medicine, today. ######################################################################## 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/
