Research workbench
Crystal structure of human NUDT5 complexed with 8-oxo-dadp and manganese
Analyse Crystal structure of human NUDT5 complexed with 8-oxo-dadp and manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ACA
- Type
- protein
- Length
- 391 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-sugar pyrophosphatase
- EC
- 3.6.1.13
- UniProt
- Q9UKK9
- Ligands
- 8DD, MN
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-sugar pyrophosphatase (EC 3.6.1.13) | protein | 196 | 23% helix, 43% strand | Q9UKK9 |
| B | ADP-sugar pyrophosphatase (EC 3.6.1.13) | protein | 195 | 22% helix, 43% strand | Q9UKK9 |
Ligands and binding sites
- 8DD · 8-oxo-7,8-dihydro-2'-deoxy-adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.73 | 0.83 | 41 | MN, 8DD |
| 2 | 457 | 0.72 | 0.82 | 45 | MN, 8DD |
| 3 | 69 | 0.29 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3197 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3ACA · Crystal structure of human NUDT5 complexed with 8-oxo-dADP and manganese · 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 3ACA · PDBe 3ACA · UniProt Q9UKK9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.