Crystal structure of dpgc with bound substrate analog and xe on oxygen diffusion pathway

Structure

x-ray diffraction · 4 distinct chains · 55% 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 · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
• XE · Xenon · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

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

Interfaces

21 interfaces between chains.

• K–L · 1502 Ų buried · 19 hydrogen bonds · protein-protein
• H–I · 1496 Ų buried · 20 hydrogen bonds · protein-protein
• B–C · 1481 Ų buried · 19 hydrogen bonds · protein-protein
• E–F · 1477 Ų buried · 18 hydrogen bonds · protein-protein
• J–K · 1458 Ų buried · 17 hydrogen bonds · protein-protein

Compared structures

• 4YLH · Crystal structure of DpgC with bound substrate analog and Xe on oxygen diffusion pathway · the same entry in another collection · chain G against G, 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 4YLH · PDBe 4YLH · UniProt Q8KLK7