Research workbench
Trypanosoma brucei PTR1 in complex with cycloguanil
Analyse Trypanosoma brucei PTR1 in complex with cycloguanil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HNC
- Type
- protein
- Length
- 993 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, 1CY
- 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, B | Pteridine reductase | protein | 249 | 47% helix, 15% strand | O76290 |
| C | Pteridine reductase | protein | 247 | 47% helix, 15% strand | O76290 |
| D | Pteridine reductase | protein | 248 | 48% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 1CY · 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine · ligand · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, C, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, C, B, 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 | 1131 | 0.83 | 0.84 | 70 | ACT, DMS |
| 2 | 653 | 0.76 | 0.82 | 50 | NAP, 1CY, GOL |
| 3 | 649 | 0.76 | 0.82 | 48 | NAP, 1CY |
| 4 | 629 | 0.76 | 0.82 | 47 | NAP, 1CY |
| 5 | 644 | 0.76 | 0.82 | 55 | NAP |
Interfaces
6 interfaces between chains.
- A–D · 1878 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1862 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1451 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1398 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 556 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6HNC · Trypanosoma brucei PTR1 in complex with cycloguanil · 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 6HNC · PDBe 6HNC · UniProt O76290
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