Research workbench
Structure of NUDT15 in complex with acyclovir monophosphate
Analyse Structure of NUDT15 in complex with acyclovir monophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B7V
- Type
- protein
- Length
- 309 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
- 4DG, MG, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.9) | protein | 154 | 21% helix, 36% strand | Q9NV35 |
| B | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.9) | protein | 155 | 21% helix, 37% strand | Q9NV35 |
Ligands and binding sites
- 4DG · 2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) methoxy]ethyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.66 | 0.87 | 31 | 4DG, MG, CL |
| 2 | 158 | 0.66 | 0.87 | 29 | 4DG, MG, CL |
| 3 | 116 | 0.39 | 0.75 | 20 | empty |
| 4 | 100 | 0.38 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1644 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7B7V · Structure of NUDT15 in complex with Acyclovir monophosphate · 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 B 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 7B7V · PDBe 7B7V · UniProt Q9NV35
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