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Pandda analysis group deposition of models with modelled events (E.G. bound ligands) -- crystal structure of NUDT5 in complex with Z239136710
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
- 5QK3
- 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
- K3A, MG, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 44% 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, 44% strand | Q9UKK9 |
| B | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 194 | 24% helix, 44% strand | Q9UKK9 |
| C | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 192 | 23% helix, 45% strand | Q9UKK9 |
| D | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 190 | 22% helix, 45% strand | Q9UKK9 |
Ligands and binding sites
- K3A · N-(5-methyl-1H-pyrazol-3-yl)acetamide · ligand · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
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 | 361 | 0.73 | 0.85 | 43 | K3A |
| 2 | 344 | 0.70 | 0.83 | 39 | MG |
| 3 | 350 | 0.70 | 0.82 | 39 | MG, EDO |
| 4 | 323 | 0.69 | 0.83 | 39 | MG |
| 5 | 61 | 0.27 | 0.72 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3173 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 3063 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 304 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5QK3 · PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)… · the same entry in another collection · chain B against B, 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 5QK3 · PDBe 5QK3 · UniProt Q9UKK9
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