MolNFT v1 · #131989 · protein
Ground-state model of NUDT5 and corresponding apo datasets for pandda analysis
5QKB · ADP-sugar pyrophosphatase: “Ground-state model of NUDT5 and corresponding apo datasets for pandda analysis”. X-ray diffraction, 2 ligands (MG, CL), 5 pockets (best druggability 0.72). MolNFT v1 #131989 on GenesisL1: 3D structure…
- PDB
- 5QKB
- Type
- protein
- Length
- 769 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
- MG, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 43% 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 | 24% 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, 42% 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 | 189 | 22% helix, 43% strand | Q9UKK9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains 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 | 349 | 0.72 | 0.84 | 44 | MG |
| 2 | 342 | 0.70 | 0.83 | 40 | empty |
| 3 | 329 | 0.70 | 0.83 | 37 | MG |
| 4 | 345 | 0.69 | 0.82 | 37 | MG |
| 5 | 54 | 0.25 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3187 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 3029 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 304 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5QKB · Ground-state model of NUDT5 and corresponding apo datasets for PanDDA analysis · 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 5QKB · PDBe 5QKB · UniProt Q9UKK9
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