Research workbench
Structure of NUDT9 complexed with ribose-5-phosphate
Analyse Structure of NUDT9 complexed with ribose-5-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QVJ
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribose pyrophosphatase
- EC
- 3.6.1.13
- UniProt
- Q9BW91
- Ligands
- RP5, MG, SO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 292 | 21% helix, 25% strand | Q9BW91 |
Ligands and binding sites
- RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.68 | 0.81 | 50 | MG, RP5 |
| 2 | 64 | 0.33 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 1QVJ · structure of NUDT9 complexed with ribose-5-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BW91 · AlphaFold monomer V2.0 prediction for ADP-ribose pyrophosphatase, mitochondrial (Q9BW91) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9BW91
- Elsewhere: RCSB PDB 1QVJ · PDBe 1QVJ · UniProt Q9BW91
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