PDBsum entry 3i5r

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protein ligands links
Protein binding PDB id
Jmol PyMol
Protein chain
81 a.a. *
Waters ×67
* Residue conservation analysis
PDB id:
Name: Protein binding
Title: Pi3k sh3 domain in complex with a peptide ligand
Structure: Phosphatidylinositol 3-kinase regulatory subunit alpha. Chain: a. Fragment: sh3 domain (unp residues 1-83). Synonym: pi3-kinase p85 subunit alpha, ptdins-3-kinase p85- alpha, pi3k. Engineered: yes. Peptide ligand. Chain: b.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: grb1, pik3r1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: artificial peptide ligand
1.70Å     R-factor:   0.184     R-free:   0.223
Authors: R.Batra-Safferling,J.Granzin,S.Modder,S.Hoffmann,D.Willbold
Key ref: R.Batra-Safferling et al. (2010). Structural studies of the phosphatidylinositol 3-kinase (PI3K) SH3 domain in complex with a peptide ligand: role of the anchor residue in ligand binding. Biol Chem, 391, 33-42. PubMed id: 19919182
06-Jul-09     Release date:   02-Mar-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P27986  (P85A_HUMAN) -  Phosphatidylinositol 3-kinase regulatory subunit alpha
724 a.a.
81 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     phosphatidylinositol 3-kinase complex   1 term 
  Biochemical function     phosphatidylinositol 3-kinase regulator activity     1 term  


Biol Chem 391:33-42 (2010)
PubMed id: 19919182  
Structural studies of the phosphatidylinositol 3-kinase (PI3K) SH3 domain in complex with a peptide ligand: role of the anchor residue in ligand binding.
R.Batra-Safferling, J.Granzin, S.Mödder, S.Hoffmann, D.Willbold.
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.