MolNFT v1 · #173095 · protein
Structure of NUDT15 in complex with ganciclovir triphosphate
7AOM · Probable 8-oxo-dgtp diphosphatase NUDT15: “Structure of NUDT15 in complex with ganciclovir triphosphate”. X-ray diffraction, 2 ligands (RQ2, MG), 2 pockets (best druggability 0.63). MolNFT v1 #173095 on GenesisL1: 3D structure…
- PDB
- 7AOM
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 8-oxo-dgtp diphosphatase NUDT15
- EC
- 3.6.1.9
- UniProt
- Q9NV35
- Ligands
- RQ2, MG
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.9) | protein | 154 | 21% helix, 34% strand | Q9NV35 |
Ligands and binding sites
- RQ2 · Ganciclovir triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.63 | 0.83 | 34 | RQ2, MG |
| 2 | 201 | 0.63 | 0.83 | 29 | RQ2, MG |
Interfaces
1 interface between chains.
- A–B · 1586 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7AOM · Structure of NUDT15 in complex with Ganciclovir triphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NV35 · AlphaFold monomer V2.0 prediction for nucleotide triphosphate diphosphatase NUDT15… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9NV35
- Elsewhere: RCSB PDB 7AOM · PDBe 7AOM · UniProt Q9NV35
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