Structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (compound AX5)

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).

Ligands and binding sites

• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
• AX5 · 6-(benzylsulfanyl)pyrimidine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 3 copies · chains B, C
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, D
• ACT · Acetate ion · additive · 2 copies · chains B, C

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

Pockets

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

Interfaces

6 interfaces between chains.

• B–D · 1887 Ų buried · 11 hydrogen bonds · protein-protein
• A–C · 1886 Ų buried · 20 hydrogen bonds · protein-protein
• C–D · 1396 Ų buried · 12 hydrogen bonds · protein-protein
• A–B · 1392 Ų buried · 11 hydrogen bonds · protein-protein
• B–C · 554 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified, 1 covalent (oxidation, additive adduct).

Compared structures

• 3BMQ · Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with… · 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 3BMQ · PDBe 3BMQ · UniProt O76290