MolNFT v1 · #119818 · protein
Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgtp, 8-oxo-dgmp and pyrophosphate (II)
5GG8 · 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), 3 pockets (best druggability 0.51).…
- PDB
- 5GG8
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- 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
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase, nudix family protein | protein | 293 | 32% helix, 33% strand | A0QUZ2 |
Ligands and binding sites
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · chains A
- 8OG · 8-oxo-2'-deoxy-guanosine-5'-monophosphate · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- MG · Magnesium ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.51 | 0.84 | 21 | empty |
| 2 | 122 | 0.44 | 0.77 | 24 | 8DG, MG |
| 3 | 72 | 0.42 | 0.81 | 14 | empty |
Compared structures
- 5GG8 · 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 A 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 5GG8 · PDBe 5GG8 · UniProt A0QUZ2
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