Research workbench
A. thaliana NUDT1 in complex with 8-oxo-dgtp
Analyse A. thaliana NUDT1 in complex with 8-oxo-dgtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FL4
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudix hydrolase 1
- EC
- 3.6.1.55, 3.6.1.67, 3.6.1.22
- UniProt
- Q9CA40
- Ligands
- 8DG, MG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22) | protein | 138 | 17% helix, 40% strand | Q9CA40 |
Ligands and binding sites
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.72 | 0.86 | 35 | MG, 8DG |
| 2 | 263 | 0.70 | 0.85 | 37 | MG, 8DG |
| 3 | 79 | 0.32 | 0.73 | 15 | empty |
| 4 | 69 | 0.28 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 Q9CA40
- Elsewhere: RCSB PDB 6FL4 · PDBe 6FL4 · UniProt Q9CA40
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