Primary Citation PubMed: 11827484
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Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation.
(2007) BMC Struct Biol 7
PubMed: 17894853 | PubMedCentral: PMC2131756 | DOI: 10.1186/1472-6807-7-58
A model of the G7-18NATE peptide was hence positioned at the peptide binding site of the crystallographically determined Grb7 SH2 domain structure by analogy to the Shc derived peptide (PSpYVNVQN) whi... h interacts with Grb 2 SH2 domain in a turn conformation (1JYR [ 52 ]) (Figure 7 ).
Publication Year: 2007
PROMALS3D web server for accurate multiple protein sequence and structure alignments.
(2008) Nucleic Acids Res 36
PubMed: 18503087 | PubMedCentral: PMC2447800 | DOI: 10.1093/nar/gkn322
This alignment is for input of four SH2 domain sequences selected from PFAM database ( 23 ) and four SH2 structures (pdb ids are 1aya, 1jyr, 1lkk and 1mil).
Publication Year: 2008
Secondary structure, a missing component of sequence-based minimotif definitions.
(2012) PLoS One 7
PubMed: 23236358 | PubMedCentral: PMC3517595 | DOI: 10.1371/journal.pone.0049957
A Centroid Algorithm was used to fit, score, and rank the similarity of the backbone and C β atoms of the xYxN ligand in the 1JYR structure with 46,593 of 57,400 xYxN structures in the PDB for... which complete structural data exists  .
A bar plot showing the distribution of centroid scores for the 46,593 xYxN structures in the PDB fit to the structure of the Grb2 SH2 peptide ligand (1JYR).
A fit of the C α backbone traces of the 203 matched structures (green lines) to the backbone trace of the xYxN structure in 1JYR (red pipe).
Minimotif consensus Binding domain Secondary structure PDB ids # lexica Instances in PDB # lexica in PDB # structured lexica in PDB # structured instances in PDB % structured lexica % structured instances xYxN SH2 β-turn 1BM2, 1BMB, 1FYR, 1JYR, 1QG1, 1TZE, 2AOB, 2H5K, 2HUW, 3IMD, 3IMJ, 3IN7, 3IN8, 3KFJ, 3N7Y, 3N84, 3N8M 400 46593 396 91 203 23% 0.44% xx[ST]x[IVL]> PDZ β-strand 2I04, 2KPL, 3NFK 48000 2926 690 257 257 37% 8.8% [ILV]QxxxRGxxx[RK] Calmodulin α–helix 1IWQ, 1MXE, 1N2D, 2BCX, 2IX7, 2K0F, 2KXW, 2L53, 2L7L, 2UX0, 2VAS, 3GOF, 3HR4, 3OXQ 3.84×10 8 73 24 5 10 21% 13.7% [RK]xxK SH3 3–10 helix 1H3H, 1OEB, 1UTI, 2DON 800 104100 794 248 797 31% 0.008% PxxPxK SH3 Polyproline helix 1CKA, 1CKB 8000 3923 549 17 39 3% 1.0% IxxNT Coiled coil 2–7 helix 2WQ0, 2WQ1, 2WQ2, 2WQ3 400 5578 276 66 378 24% 6.8% >indicates that the motif must be on the C-terminus.
Publication Year: 2012
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