MolNFT v1 · #131948 · protein
Pandda analysis group deposition of models with modelled events (E.G. bound ligands) -- crystal structure of NUDT5 in complex with Z1614545742
5QJ6 · ADP-sugar pyrophosphatase: “Pandda analysis group deposition of models with modelled events (E.G. bound ligands) -- crystal structure of…”. X-ray diffraction, 2 ligands (GQJ, MG), 5 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5QJ6
- 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
- GQJ, MG
- 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, 43% 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, 43% strand | Q9UKK9 |
| D | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 190 | 22% helix, 46% strand | Q9UKK9 |
Ligands and binding sites
- GQJ · methyl (2~{S},4~{R})-1-(furan-2-ylcarbonyl)-4-oxidanyl-pyrrolidine-2-carboxylate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- 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
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 | 357 | 0.73 | 0.85 | 44 | MG, EDO |
| 2 | 344 | 0.70 | 0.83 | 39 | MG, EDO |
| 3 | 324 | 0.68 | 0.82 | 38 | MG, EDO |
| 4 | 257 | 0.65 | 0.82 | 39 | MG, EDO |
| 5 | 52 | 0.25 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3203 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 3054 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 310 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5QJ6 · 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 5QJ6 · PDBe 5QJ6 · UniProt Q9UKK9
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