Trypanosoma brucei PTR1 in complex with inhibitor WH16

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).

Ligands and binding sites

• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
• W16 · 5-(2-chloroethyl)-1,3,4-thiadiazol-2-amine · ligand · 4 copies · chains A, B, C, D
• DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · chains A, C
• ACT · Acetate ion · additive · 2 copies · chains A, D
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, C, B, D
• DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains B, D

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

Pockets

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

Interfaces

6 interfaces between chains.

• C–D · 1860 Ų buried · 10 hydrogen bonds · protein-protein
• A–B · 1844 Ų buried · 10 hydrogen bonds · protein-protein
• B–C · 1406 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 1400 Ų buried · 11 hydrogen bonds · protein-protein
• B–D · 558 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 2 modified (additive adduct, oxidation, covalent ligand).

Compared structures

• 2YHI · Trypanosoma brucei PTR1 in complex with inhibitor WH16 · 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 Q581W1
• Elsewhere: RCSB PDB 2YHI · PDBe 2YHI · UniProt Q581W1