Research workbench
Trypanosoma brucei PTR1 in complex with inhibitor 9
Analyse Trypanosoma brucei PTR1 in complex with inhibitor 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WCF
- Type
- protein
- Length
- 992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, 3KN
- 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 | 249 | 47% helix, 15% strand | O76290 |
| B | Pteridine reductase | protein | 247 | 48% helix, 15% strand | O76290 |
| C | Pteridine reductase | protein | 246 | 47% helix, 15% strand | O76290 |
| D | Pteridine reductase | protein | 250 | 48% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 3KN · 3-(5-amino-1,3,4-thiadiazol-2-yl)pyridin-4-amine · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 1158 | 0.83 | 0.84 | 73 | empty |
| 2 | 598 | 0.76 | 0.82 | 46 | NAP, 3KN |
| 3 | 612 | 0.76 | 0.82 | 47 | NAP, 3KN |
| 4 | 636 | 0.76 | 0.82 | 53 | NAP, 3KN |
| 5 | 562 | 0.76 | 0.83 | 47 | NAP, 3KN |
Interfaces
6 interfaces between chains.
- B–D · 1866 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1836 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1408 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1385 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 562 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (oxidation).
Compared structures
- 4WCF · Trypanosoma brucei PTR1 in complex with inhibitor 9 · 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 4WCF · PDBe 4WCF · UniProt O76290
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