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
- 5GG6
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, nudix family protein
- UniProt
- A0QUZ2
- Ligands
- 8DG, MG, CL
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase, nudix family protein | protein | 290 | 34% helix, 34% strand | A0QUZ2 |
| B | Hydrolase, nudix family protein | protein | 295 | 33% helix, 33% strand | A0QUZ2 |
Ligands and binding sites
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.63 | 0.74 | 63 | CL |
| 2 | 113 | 0.48 | 0.80 | 25 | EDO |
| 3 | 100 | 0.47 | 0.80 | 25 | empty |
| 4 | 96 | 0.46 | 0.80 | 14 | empty |
| 5 | 103 | 0.46 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 133 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5GG6 · 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 5GG6 · PDBe 5GG6 · UniProt A0QUZ2
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