Research workbench
Crystal structure of mycobacterium smegmatis MUTT1 in complex with ATP, magnesium fluoride and phosphate
Analyse Crystal structure of mycobacterium smegmatis MUTT1 in complex with ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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