MolNFT v1 · #123224 · protein
Trypanosoma brucei PTR1 in complex with cofactor and inhibitor nmt- H024 (compound 2)
5JDI · Pteridine reductase: “Trypanosoma brucei PTR1 in complex with cofactor and inhibitor nmt- H024 (compound 2)”. X-ray diffraction, 2 ligands (NAP, 6JO), 7 pockets (best druggability 0.83). MolNFT v1 #123224 on GenesisL1: 3D structure…
- PDB
- 5JDI
- Type
- protein
- Length
- 984 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, 6JO
- 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 | 240 | 50% 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
- 6JO · 3,6-dihydroxy-2-(3-hydroxyphenyl)-4H-1-benzopyran-4-one · ligand · 3 copies · chains A, B, D
- ACT · Acetate ion · additive · 3 copies · chains A, C
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 | 1124 | 0.83 | 0.84 | 69 | empty |
| 2 | 647 | 0.77 | 0.82 | 47 | NAP, 6JO |
| 3 | 611 | 0.76 | 0.82 | 48 | NAP, 6JO |
| 4 | 606 | 0.76 | 0.82 | 49 | NAP, 6JO |
| 5 | 472 | 0.67 | 0.78 | 42 | NAP |
Interfaces
6 interfaces between chains.
- A–C · 1870 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1848 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1440 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1419 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 560 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5JDI · Trypanosoma brucei PTR1 in complex with cofactor and inhibitor NMT-H024 (compound 2) · 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 5JDI · PDBe 5JDI · UniProt O76290
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