Research workbench
Trypanosoma brucei PTR1 in complex with inhibitor np-29
Analyse Trypanosoma brucei PTR1 in complex with inhibitor np-29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JCX
- Type
- protein
- Length
- 984 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, CC6
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pteridine reductase | protein | 249 | 47% helix, 14% strand | O76290 |
| B | Pteridine reductase | protein | 248 | 48% helix, 15% strand | O76290 |
| C | Pteridine reductase | protein | 238 | 47% helix, 16% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, D
- CC6 · 3,5,7-trihydroxy-2-(2-hydroxyphenyl)-4H-1-benzopyran-4-one · ligand · 3 copies · chains A, B, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
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 | 1156 | 0.83 | 0.84 | 70 | empty |
| 2 | 574 | 0.75 | 0.82 | 49 | NAP, CC6 |
| 3 | 605 | 0.75 | 0.82 | 49 | NAP, CC6 |
| 4 | 595 | 0.75 | 0.82 | 47 | NAP, CC6 |
| 5 | 383 | 0.60 | 0.76 | 45 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1863 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1832 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1443 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1426 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 560 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5JCX · Trypanosoma brucei PTR1 in complex with inhibitor NP-29 · 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 5JCX · PDBe 5JCX · UniProt O76290
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