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

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 28% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
• U67 · 4-methylpentan-1-amine · ligand · 2 copies · chains A, C, B, D
• CA · Calcium ion · metal · chains A
• NA · Sodium ion · metal · chains A, B
• IPA · Isopropyl alcohol · additive · 2 copies · chains A, C, B

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

Interfaces

3 interfaces between chains.

• A–B · 1118 Ų buried · 18 hydrogen bonds · protein-protein
• A–C · 388 Ų buried · 11 hydrogen bonds · protein-protein
• B–D · 379 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6WO2 · Crystal Structure of the Grb2 SH2 Domain in Complex with a Tripeptide… · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.94

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 6WO2 · PDBe 6WO2 · UniProt P62993