Trypanosoma brucei PTR1 in complex with inhibitor np-13 (hesperetin)

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).

Ligands and binding sites

• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
• 6JP · (2S)-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydro-4H-1-benzopyran-4-one · ligand · 4 copies · chains A, D, B, C
• ACT · Acetate ion · additive · 2 copies · chains A, C
• GOL · Glycerol · additive · chains C

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–D · 1888 Ų buried · 17 hydrogen bonds · protein-protein
• A–C · 1852 Ų buried · 17 hydrogen bonds · protein-protein
• C–D · 1414 Ų buried · 9 hydrogen bonds · protein-protein
• A–B · 1398 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 564 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (oxidation).

Compared structures

• 5JDC · Trypanosoma brucei PTR1 in complex with inhibitor NP-13 (Hesperetin) · the same entry in another collection · chain A 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 O76290
• Elsewhere: RCSB PDB 5JDC · PDBe 5JDC · UniProt O76290