Research workbench
Trypanosoma brucei PTR1 in complex with inhibitor 10
Analyse Trypanosoma brucei PTR1 in complex with inhibitor 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WCD
- Type
- protein
- Length
- 989 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, 3KH
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pteridine reductase | protein | 250 | 47% helix, 14% strand | O76290 |
| C | Pteridine reductase | protein | 240 | 47% helix, 15% strand | O76290 |
| D | Pteridine reductase | protein | 249 | 47% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, D
- 3KH · 5-(1H-benzotriazol-6-yl)-1,3,4-thiadiazol-2-amine · ligand · 3 copies · chains A, B, D
- ACT · Acetate ion · additive · 3 copies · chains A, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.84 | 0.84 | 70 | empty |
| 2 | 625 | 0.78 | 0.83 | 47 | NAP, 3KH |
| 3 | 639 | 0.76 | 0.82 | 51 | NAP, 3KH |
| 4 | 591 | 0.75 | 0.82 | 47 | NAP, 3KH |
| 5 | 291 | 0.61 | 0.79 | 30 | ACT |
Interfaces
6 interfaces between chains.
- B–D · 1873 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1862 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1447 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1421 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 561 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4WCD · Trypanosoma brucei PTR1 in complex with inhibitor 10 · 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 4WCD · PDBe 4WCD · UniProt O76290
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