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Structural and population-based evaluations of TBC1D1 p.Arg125Trp.
(2013) PLoS One 8
PubMed: 23667688 | PubMedCentral: PMC3646766 | DOI: 10.1371/journal.pone.0063897
The best available template for homology modelling TBC1D1 PTB1, the PTB domain of AIDA1 (2M38; DOI:10.2210/pdb2m38/pdb), has a sequence identity of 24% which is a little lower than the requiredȦ... ;30% required for reliable fold identification from a single template.
Shown in yellow is the PTB domain of AIDA1 (2M38; DOI:10.2210/pdb2m38/pdb) which has the highest (24%) amino acid sequence identity to the TBC1D1 PTB1 domain.
For example, the HHpred E-values for the top 10 template structures are between 10 −36 and 10 −33 and the average of the Cα Root-mean-square deviation (RMSD) between models built with these templates and 2M38 is 2.25 Å, i.e. the same fold in each case.
Publication Year: 2013
Solution structure and peptide binding of the PTB domain from the AIDA1 postsynaptic signaling scaffolding protein.
PubMed: 23799029 | PubMedCentral: PMC3683042 | DOI: 10.1371/journal.pone.0065605
The top 15 structures according to lowest refinement energy was deposited as an ensemble in the Protein Data Bank with the accession code 2M38.
PDB Protein Source RMSD Aligned Identity Reference 2M38 AIDA1 NMR 0.0 Å 134 aa 100% this study 1AQC X11+ APP peptide X-ray 1.4 Å 109 aa 26%  1P3R DAB1 X-ray 1.6 Å 115 aa 27%  2ELA APPL1 X-ray 1.7 Å 121 aa 16%  3DXC Fe65+ APP peptide X-ray 1.8 Å 120 aa 20%  Structural and biochemical investigations of the Fe65 PTB2 domain demonstrated >100-fold difference in affinity between an 11 aa.
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