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PDBsum entry 3i5s
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Protein binding
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PDB id
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3i5s
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References listed in PDB file
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Key reference
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Title
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Structural studies of the phosphatidylinositol 3-Kinase (pi3k) sh3 domain in complex with a peptide ligand: role of the anchor residue in ligand binding.
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Authors
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R.Batra-Safferling,
J.Granzin,
S.Mödder,
S.Hoffmann,
D.Willbold.
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Ref.
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Biol Chem, 2010,
391,
33-42.
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PubMed id
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Abstract
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Src homology 3 (SH3) domains are mediators of protein-protein interactions. They
comprise approximately 60 amino acid residues and are found in many
intracellular signaling proteins. Here, we present the crystal structure of the
SH3 domain from phosphatidylinositol 3-kinase (PI3K) in complex with the
12-residue proline-rich peptide PD1R (HSKRPLPPLPSL). The crystal structure of
the PI3K SH3-PD1R complex at a resolution of 1.7 A reveals type I ligand
orientation of the bound peptide with an extended conformation where the central
portion forms a left-handed type II polyproline (PPII) helix. The overall
structure of the SH3 domain shows minimal changes on ligand binding. In
addition, we also attempted crystallization with another peptide ligand (PD1)
where the residue at anchor position P(-3) is a tyrosine. The crystals obtained
did not contain the PD1 ligand; instead, the ligand binding site is partially
occupied by residues Arg18 and Trp55 from the symmetry-related PI3K SH3
molecule. Considering these crystal structures of PI3K SH3 together with
published reports, we provide a comparative analysis of protein-ligand
interactions that has helped us identify the individual residues which play an
important role in defining target specificity.
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