Research workbench
Trypanosoma brucei PTR1 in complex with inhibitor 3A (F020)
Analyse Trypanosoma brucei PTR1 in complex with inhibitor 3A (F020) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GCL
- Type
- protein
- Length
- 996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, EUE
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase | protein | 250 | 47% helix, 15% strand | O76290 |
| B, D | Pteridine reductase | protein | 249 | 46% helix, 15% strand | O76290 |
| C | Pteridine reductase | protein | 248 | 47% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- EUE · 6-methylsulfonyl-1,3-benzothiazol-2-amine · 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 | 1142 | 0.83 | 0.84 | 71 | empty |
| 2 | 649 | 0.78 | 0.83 | 51 | NAP, EUE |
| 3 | 590 | 0.77 | 0.83 | 47 | NAP, EUE |
| 4 | 624 | 0.77 | 0.82 | 49 | NAP, EUE |
| 5 | 575 | 0.76 | 0.82 | 47 | NAP, EUE |
Interfaces
6 interfaces between chains.
- B–D · 1857 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1847 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1452 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1427 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 554 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6GCL · Trypanosoma brucei PTR1 in complex with inhibitor 3a (F020) · 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 6GCL · PDBe 6GCL · UniProt O76290
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