MolNFT v1 · #156528 · protein
Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgdp
6M72 · Hydrolase, nudix family protein: “Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgdp”. X-ray diffraction, 3 ligands (8GD, POP, MG), 3 pockets (best druggability 0.49). MolNFT v1 #156528 on GenesisL1: 3D…
- PDB
- 6M72
- Type
- protein
- Length
- 291 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, nudix family protein
- UniProt
- A0QUZ2
- Ligands
- 8GD, POP, MG
- Pockets
- 3 · best druggability 0.49
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 | 291 | 34% helix, 34% strand | A0QUZ2 |
Ligands and binding sites
- 8GD · 2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate) · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.49 | 0.80 | 25 | empty |
| 2 | 133 | 0.42 | 0.76 | 26 | 8GD, MG |
| 3 | 100 | 0.41 | 0.77 | 17 | empty |
Compared structures
- 6M72 · Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP · 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 6M72 · PDBe 6M72 · UniProt A0QUZ2
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