Research workbench
Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6,7,7- trimethyl-7,8-dihydropteridine-2,4-diamine (DX3)
Analyse Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JQ8
- Type
- protein
- Length
- 988 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, DX3
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase 1 (EC 1.5.1.33) | protein | 248 | 48% helix, 14% strand | Q581W1 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 248 | 47% helix, 14% strand | Q581W1 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 243 | 49% helix, 14% strand | Q581W1 |
| D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 249 | 47% helix, 15% strand | Q581W1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- DX3 · 6,7,7-trimethyl-7,8-dihydropteridine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.83 | 0.84 | 69 | empty |
| 2 | 595 | 0.77 | 0.83 | 50 | NAP, DX3 |
| 3 | 596 | 0.76 | 0.82 | 48 | NAP, DX3 |
| 4 | 605 | 0.74 | 0.81 | 48 | NAP, DX3 |
| 5 | 594 | 0.71 | 0.79 | 48 | NAP, DX3 |
Interfaces
6 interfaces between chains.
- A–B · 1843 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1841 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1426 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1405 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 561 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 3JQ8 · 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 3JQ8 · PDBe 3JQ8 · UniProt Q581W1
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