Crystal structure of escherichia COLI semet substituted glycerol-3- phosphate dehydrogenase in complex with dhap

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).

Ligands and binding sites

• BCN · Bicine · ligand · 3 copies · chains A, B
• FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
• 13P · 1,3-dihydroxyacetonephosphate · ligand · 2 copies · chains A, B
• TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A, B
• PO4 · Phosphate ion · ion · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 26 copies · chains A, B
• BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains A, B
• IMD · Imidazole · additive · 6 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 778 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

• 2R4J · Crystal structure of Escherichia coli SeMet substituted Glycerol-3-phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
• P13035 · AlphaFold monomer V2.0 prediction for aerobic glycerol-3-phosphate dehydrogenase (P13035) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P13035
• Elsewhere: RCSB PDB 2R4J · PDBe 2R4J · UniProt P13035