Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 1,3,5- triazine-2,4,6-triamine (AX2)

Structure

x-ray diffraction · 2 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
• AX2 · 1,3,5-triazine-2,4,6-triamine · ligand · 4 copies · chains A, B, C, D
• D1D · (4S,5S)-1,2-dithiane-4,5-diol · ligand · 4 copies · chains A, B, C, D
• ACT · Acetate ion · additive · 6 copies · chains A, B, C, D
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 5 copies · chains A, D, B, C
• GOL · Glycerol · additive · 2 copies · chains A, 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 · 1854 Ų buried · 13 hydrogen bonds · protein-protein
• A–C · 1842 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 1448 Ų buried · 14 hydrogen bonds · protein-protein
• C–D · 1405 Ų buried · 12 hydrogen bonds · protein-protein
• A–D · 556 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 1 modified (additive adduct, oxidation).

Compared structures

• 3JQF · Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary… · the same entry in another collection · chain C against C, 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 3JQF · PDBe 3JQF · UniProt Q581W1