Structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (compound AX4)

Structure

x-ray diffraction · 4 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
• AX4 · 6-[(4-methylphenyl)sulfanyl]pyrimidine-2,4-diamine · 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
• NA · Sodium ion · metal · chains A
• ACT · Acetate ion · additive · 7 copies · chains A, B, C, D
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 4 copies · chains A, D, B, C
• GOL · Glycerol · additive · 3 copies · chains A, B

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.

• A–C · 1917 Ų buried · 25 hydrogen bonds · protein-protein
• B–D · 1832 Ų buried · 12 hydrogen bonds · protein-protein
• C–D · 1394 Ų buried · 12 hydrogen bonds · protein-protein
• A–B · 1389 Ų buried · 12 hydrogen bonds · protein-protein
• A–D · 554 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 3BMO · 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 3BMO · PDBe 3BMO · UniProt O76290