Research workbench
PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with FS-1169
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
- 5QTQ
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Homo sapiens
- Molecule
- ADP-sugar pyrophosphatase
- EC
- 3.6.1.13, 3.6.1.58, 2.7.7.96
- UniProt
- Q9UKK9
- Ligands
- PWM, MG, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.82 · 4 distinct chains · 22% 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 | 23% helix, 44% strand | Q9UKK9 |
| B | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 195 | 22% helix, 42% strand | Q9UKK9 |
| C | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 193 | 23% helix, 42% strand | Q9UKK9 |
| D | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 194 | 20% helix, 42% strand | Q9UKK9 |
Ligands and binding sites
- PWM · 5-fluoroquinazolin-4(3H)-one · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains 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
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 | 307 | 0.72 | 0.85 | 39 | EDO, PWM, MG |
| 2 | 363 | 0.72 | 0.84 | 41 | PWM, EDO, MG |
| 3 | 358 | 0.71 | 0.83 | 42 | EDO, PWM |
| 4 | 317 | 0.70 | 0.84 | 38 | MG, EDO, PWM |
| 5 | 79 | 0.31 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3165 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 3135 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 327 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5QTQ · Pandda analysis group deposition -- crystal structure of NUDT5 in complex with fs-1169 · 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 5QTQ · PDBe 5QTQ · UniProt Q9UKK9
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