Crystal structure of R254K mutanat of dpgc with bound substrate analog

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).

Ligands and binding sites

• YE1 · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-4-({3-[(2-{[(3,5-dihydroxyphenyl)acetyl]amino}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate · ligand · 3 copies · chains A, B, C
• OXY · Oxygen molecule · ion · 2 copies · chains A, C

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

Pockets

17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1475 Ų buried · 21 hydrogen bonds · protein-protein
• B–C · 1456 Ų buried · 18 hydrogen bonds · protein-protein
• A–C · 1445 Ų buried · 17 hydrogen bonds · protein-protein

Compared structures

• 2PG8 · Crystal structure of R254K mutanat of DpgC with bound substrate analog · the same entry in another collection · chain A against A, TM-score 1.00
• Q8KLK7 · AlphaFold monomer V2.0 prediction for (3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase… · a predicted model of the same protein · chain B against A, TM-score 1.00

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 Q8KLK7
• Elsewhere: RCSB PDB 2PG8 · PDBe 2PG8 · UniProt Q8KLK7