Crystal structure of an N-terminal deletion mutant of escherichia COLI gadb in an autoinhibited state (aldamine)

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).

Ligands and binding sites

• PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
• SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
• EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, F, D, E

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Interfaces

12 interfaces between chains.

• E–F · 5727 Ų buried · 89 hydrogen bonds · protein-protein
• A–B · 5571 Ų buried · 80 hydrogen bonds · protein-protein
• C–D · 5526 Ų buried · 76 hydrogen bonds · protein-protein
• A–F · 1277 Ų buried · 11 hydrogen bonds · protein-protein
• B–C · 1239 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 cofactor (pyridoxal phosphate Schiff base).

Compared structures

• 2DGK · Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an… · the same entry in another collection · chain F against F, TM-score 1.00
• P69910 · AlphaFold monomer V2.0 prediction for glutamate decarboxylase beta (P69910) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P69910
• Elsewhere: RCSB PDB 2DGK · PDBe 2DGK · UniProt P69910