Research workbench
Pandda analysis group deposition -- crystal structure of NUDT5 in complex with ss-4432
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
- 5QTN
- Type
- protein
- Length
- 775 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
- PWD, MG, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 22% 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 | 22% 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, 44% strand | Q9UKK9 |
| C | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 193 | 23% helix, 41% 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
- PWD · 5-fluoro-1H-pyrrolo[2,3-b]pyridine · ligand · 3 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, 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 | 0.72 | 0.84 | 51 | PWD, MG |
| 2 | 323 | 0.70 | 0.84 | 38 | MG, EDO, PWD |
| 3 | 330 | 0.68 | 0.82 | 44 | MG, PWD |
| 4 | 261 | 0.65 | 0.82 | 39 | MG |
| 5 | 57 | 0.27 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3169 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 3073 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 319 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5QTN · PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with SS-4432 · 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 5QTN · PDBe 5QTN · UniProt Q9UKK9
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