MolNFT v1 · #114411 · protein
Crystal structure of human NUDT15 (MTH2)
5BON · Probable 8-oxo-dgtp diphosphatase NUDT15: “Crystal structure of human NUDT15 (MTH2)”. X-ray diffraction, 1 ligand (MG), 17 pockets (best druggability 0.83). MolNFT v1 #114411 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5BON
- Type
- protein
- Length
- 1,227 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 8-oxo-dgtp diphosphatase NUDT15
- EC
- 3.6.1.55
- UniProt
- Q9NV35
- Ligands
- MG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.55) | protein | 156 | 21% helix, 36% strand | Q9NV35 |
| B, E | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.55) | protein | 154 | 21% helix, 36% strand | Q9NV35 |
| C, F, H | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.55) | protein | 155 | 21% helix, 36% strand | Q9NV35 |
| D, G | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.55) | protein | 149 | 22% helix, 38% strand | Q9NV35 |
Ligands and binding sites
- MG · Magnesium ion · metal · 32 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.83 | 0.86 | 80 | MG |
| 2 | 846 | 0.74 | 0.78 | 74 | empty |
| 3 | 127 | 0.70 | 0.91 | 21 | empty |
| 4 | 390 | 0.67 | 0.81 | 45 | MG |
| 5 | 187 | 0.67 | 0.86 | 32 | MG |
Interfaces
14 interfaces between chains.
- E–F · 1662 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1608 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1447 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1441 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 464 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 5BON · PDBe 5BON · UniProt Q9NV35
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