Research workbench
Trypanosoma brucei PTR1 (TBPTR1) in complex with pyrimethamine
Analyse Trypanosoma brucei PTR1 (TBPTR1) in complex with pyrimethamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OPJ
- Type
- protein
- Length
- 990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, CP6
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase | protein | 250 | 47% helix, 15% strand | O76290 |
| B | Pteridine reductase | protein | 248 | 48% helix, 15% strand | O76290 |
| C | Pteridine reductase | protein | 243 | 48% helix, 15% strand | O76290 |
| D | Pteridine reductase | protein | 249 | 48% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- CP6 · 5-(4-chloro-phenyl)-6-ethyl-pyrimidine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · 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 | 1096 | 0.83 | 0.84 | 68 | empty |
| 2 | 659 | 0.76 | 0.82 | 50 | NAP, CP6 |
| 3 | 635 | 0.76 | 0.82 | 47 | NAP, CP6 |
| 4 | 594 | 0.75 | 0.82 | 46 | NAP, CP6 |
| 5 | 606 | 0.73 | 0.80 | 55 | NAP, CP6 |
Interfaces
6 interfaces between chains.
- A–C · 1861 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1856 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1414 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1398 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 556 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7OPJ · Trypanosoma brucei PTR1 (TbPTR1) in complex with pyrimethamine · 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 7OPJ · PDBe 7OPJ · UniProt O76290
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