MolNFT v1 · #119817 · protein
Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgtp, 8-oxo-dgmp and pyrophosphate (I)
5GG7 · Hydrolase, nudix family protein: “Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgtp, 8-oxo-dgmp and pyrophosphate…”. X-ray diffraction, 4 ligands (8DG, 8OG, POP), 6 pockets (best druggability 0.50).…
- PDB
- 5GG7
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, nudix family protein
- UniProt
- A0QUZ2
- Ligands
- 8DG, 8OG, POP, MG
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase, nudix family protein | protein | 291 | 33% helix, 33% strand | A0QUZ2 |
| B | Hydrolase, nudix family protein | protein | 290 | 33% helix, 34% strand | A0QUZ2 |
Ligands and binding sites
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- 8OG · 8-oxo-2'-deoxy-guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.50 | 0.83 | 15 | empty |
| 2 | 134 | 0.48 | 0.78 | 27 | empty |
| 3 | 88 | 0.45 | 0.80 | 15 | empty |
| 4 | 74 | 0.41 | 0.79 | 17 | empty |
| 5 | 57 | 0.34 | 0.78 | 14 | 8DG |
Interfaces
1 interface between chains.
- A–B · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GG7 · Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP, 8-oxo-dGMP… · 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 B against A, TM-score 0.97
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 5GG7 · PDBe 5GG7 · UniProt A0QUZ2
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