Crystal structure of the VAV2 SH2 domain in complex with txnip phosphorylated peptide

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 29% strand (DSSP).

Ligands and binding sites

• UNX · Unknown atom or ion · ion · 14 copies · chains A, D, B, C, F
• NH2 · Amino group · ion · chains D

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• B–E · 438 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 432 Ų buried · 10 hydrogen bonds · protein-protein
• C–F · 390 Ų buried · 10 hydrogen bonds · protein-protein
• B–C · 239 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 217 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 1 disulfide (phosphorylation, disulfide).

Compared structures

• 4ROJ · Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide · the same entry in another collection · chain F against F, TM-score 1.00
• P52735 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange factor VAV2 (P52735) · a predicted model of the same protein · chain A against A, TM-score 0.99
• Q9H3M7 · AlphaFold monomer V2.0 prediction for thioredoxin-interacting protein (Q9H3M7) · a predicted model of the same protein · chain E against A, TM-score 0.53

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 P52735
• Every structure of UniProt Q9H3M7
• Elsewhere: RCSB PDB 4ROJ · PDBe 4ROJ · UniProt P52735 · UniProt Q9H3M7