MolNFT v1 · #139351 · protein
Crystal structure of mycobacterium smegmatis MUTT1 in complex with ATP, magnesium fluoride and phosphate
5XD5 · Hydrolase, nudix family protein: “Crystal structure of mycobacterium smegmatis MUTT1 in complex with ATP, magnesium fluoride and phosphate”. X-ray diffraction, 5 ligands (ATP, MG, CL), 8 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 5XD5
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, nudix family protein
- UniProt
- A0QUZ2
- Ligands
- ATP, MG, CL, F, PO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hydrolase, nudix family protein | protein | 289 | 35% helix, 33% strand | A0QUZ2 |
| A | Hydrolase, nudix family protein | protein | 289 | 34% helix, 34% strand | A0QUZ2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 8 copies · chains B, A
- CL · Chloride ion · ion · 7 copies · chains B, A
- F · Fluoride ion · ion · 6 copies · chains B, A
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 7 copies · chains B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.70 | 0.78 | 67 | empty |
| 2 | 122 | 0.66 | 0.89 | 22 | empty |
| 3 | 252 | 0.58 | 0.79 | 31 | GOL |
| 4 | 73 | 0.44 | 0.81 | 17 | GOL |
| 5 | 92 | 0.42 | 0.78 | 21 | ATP, MG, F |
Interfaces
1 interface between chains.
- B–A · 821 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5XD5 · Crystal structure of Mycobacterium smegmatis MutT1 in complex with ATP, magnesium… · the same entry in another collection · chain B against B, 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 0.99
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 5XD5 · PDBe 5XD5 · UniProt A0QUZ2
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