Crystal structure of the GRB2 SH2 domain in complex with a tripeptide: ac-py-AC6C-N-phenylpropyl

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 29% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains B, C, D
• PRA · 3-phenylpropylamine · ligand · 2 copies · chains A, B, C, D
• CA · Calcium ion · metal · chains C
• CL · Chloride ion · ion · chains C, D
• GOL · Glycerol · additive · 2 copies · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 1219 Ų buried · 23 hydrogen bonds · protein-protein
• A–B · 362 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 351 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard, phosphorylation).

Compared structures

• 6WM1 · Crystal structure of the Grb2 SH2 domain in complex with a tripeptide… · the same entry in another collection · chain A against A, TM-score 1.00
• P62993 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 2 (P62993) · a predicted model of the same protein · chain C against A, TM-score 0.95

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P62993
• Elsewhere: RCSB PDB 6WM1 · PDBe 6WM1 · UniProt P62993