MolNFT v1 · #68252 · protein
Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-6-(1,3-benzodioxol-5-yl)-4-oxo-4,7- dihydro-3H-PYRROLO[2,3-D]PYRIMIDINE-5-carbonitrile (AX1)
3JQ9: “Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor…”. X-ray diffraction, 2 ligands (NAP, AX1), 7 pockets (best druggability 0.83). MolNFT v1 #68252 on GenesisL1: 3D structure…
- PDB
- 3JQ9
- Type
- protein
- Length
- 995 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase 1
- EC
- 1.5.1.33
- UniProt
- Q581W1
- Ligands
- NAP, AX1
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 249 | 47% helix, 15% strand | Q581W1 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 248 | 45% helix, 15% strand | Q581W1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- AX1 · 2-amino-6-(1,3-benzodioxol-5-yl)-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile · ligand · 4 copies · chains A, B, C, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.83 | 0.84 | 69 | empty |
| 2 | 617 | 0.77 | 0.83 | 48 | NAP, AX1 |
| 3 | 626 | 0.77 | 0.83 | 50 | NAP, AX1 |
| 4 | 618 | 0.77 | 0.83 | 47 | NAP, AX1 |
| 5 | 587 | 0.76 | 0.83 | 51 | NAP, AX1 |
Interfaces
6 interfaces between chains.
- A–B · 1873 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1840 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1421 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1410 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 573 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3JQ9 · Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary… · 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 3JQ9 · PDBe 3JQ9 · UniProt Q581W1
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