Research workbench
Pandda analysis group deposition -- crystal structure of NUDT5 in complex with gb-0804
Analyse Pandda analysis group deposition -- crystal structure of NUDT5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QTL
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NUDT5
- UniProt
- Q9UKK9
- Ligands
- PW7, MG, CL
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NUDT5 | protein | 194 | 23% helix, 44% strand | Q9UKK9 |
| B | NUDT5 | protein | 195 | 24% helix, 42% strand | Q9UKK9 |
| C | NUDT5 | protein | 193 | 23% helix, 42% strand | Q9UKK9 |
| D | NUDT5 | protein | 194 | 20% helix, 42% strand | Q9UKK9 |
Ligands and binding sites
- PW7 · 4-(trifluoromethyl)pyrimidin-2-amine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.70 | 0.84 | 40 | EDO, PW7, MG |
| 2 | 327 | 0.70 | 0.83 | 41 | MG, EDO, PW7 |
| 3 | 321 | 0.70 | 0.83 | 41 | PW7, MG, EDO |
| 4 | 344 | 0.69 | 0.83 | 38 | MG, EDO, PW7 |
| 5 | 76 | 0.29 | 0.72 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3179 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 3177 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 304 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5QTL · PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with GB-0804 · 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 Q9UKK9
- Elsewhere: RCSB PDB 5QTL · PDBe 5QTL · UniProt Q9UKK9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.