Research workbench
Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgtp
Analyse Crystal structure of mycobacterium smegmatis MUTT1 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
- 6M6Y
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, nudix family protein
- UniProt
- A0QUZ2
- Ligands
- 8DG, POP, MG, PO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase, nudix family protein | protein | 292 | 34% helix, 34% strand | A0QUZ2 |
Ligands and binding sites
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.45 | 0.79 | 26 | empty |
| 2 | 109 | 0.44 | 0.78 | 15 | empty |
| 3 | 129 | 0.43 | 0.76 | 21 | 8DG, PO4, MG |
Compared structures
- 6M6Y · Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP · the same entry in another collection · chain A against A, TM-score 1.00
- A0QUZ2 · AlphaFold monomer V2.0 prediction for 8-oxo-(D)GTP phosphatase (A0QUZ2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A0QUZ2
- Elsewhere: RCSB PDB 6M6Y · PDBe 6M6Y · UniProt A0QUZ2
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