Research workbench
Trypanosoma brucei PTR1 (TBPTR1) in complex with inhibitor 4 (nmt- C0026)
Analyse Trypanosoma brucei PTR1 (TBPTR1) in complex with inhibitor 4 (nmt- C0026) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RX6
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, KMK
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase | protein | 248 | 48% helix, 15% strand | O76290 |
| B, D | Pteridine reductase | protein | 247 | 48% helix, 15% strand | O76290 |
| C | Pteridine reductase | protein | 244 | 48% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- KMK · methyl 1-[4-[[2,4-bis(azanyl)pteridin-6-yl]methyl-(3-oxidanylpropyl)amino]phenyl]carbonylpiperidine-4-carboxylate · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains B
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 | 1197 | 0.84 | 0.85 | 70 | empty |
| 2 | 612 | 0.76 | 0.82 | 50 | NAP, KMK |
| 3 | 616 | 0.76 | 0.82 | 51 | NAP, KMK |
| 4 | 577 | 0.75 | 0.82 | 48 | NAP, KMK |
| 5 | 596 | 0.75 | 0.81 | 50 | NAP, KMK |
Interfaces
6 interfaces between chains.
- A–C · 1848 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1842 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1406 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1388 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 548 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6RX6 · Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 4 (NMT-C0026) · 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 6RX6 · PDBe 6RX6 · UniProt O76290
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