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Pandda analysis group deposition of models with modelled events (E.G. bound ligands) -- crystal structure of NUDT5 in complex with Z2377835233
Analyse Pandda analysis group deposition of models with modelled events (E.G. bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QKA
- Type
- protein
- Length
- 770 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-sugar pyrophosphatase
- EC
- 3.6.1.13, 3.6.1.58, 2.7.7.96
- UniProt
- Q9UKK9
- Ligands
- K3Y, MG, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 194 | 23% helix, 42% strand | Q9UKK9 |
| B | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 194 | 24% helix, 43% strand | Q9UKK9 |
| C | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 192 | 23% helix, 38% strand | Q9UKK9 |
| D | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 190 | 21% helix, 43% strand | Q9UKK9 |
Ligands and binding sites
- K3Y · 1-methyl-3-[(3R)-piperidin-3-yl]-1H-pyrazole-4-carboxamide · ligand · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.73 | 0.85 | 44 | MG |
| 2 | 379 | 0.69 | 0.82 | 45 | MG |
| 3 | 271 | 0.69 | 0.84 | 41 | MG, EDO |
| 4 | 347 | 0.69 | 0.82 | 41 | MG, K3Y, EDO |
| 5 | 50 | 0.25 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3213 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 3074 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5QKA · PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)… · 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 5QKA · PDBe 5QKA · UniProt Q9UKK9
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