Research workbench
Crystal structure of mycobacterium smegmatis MUTT1 in complex with AP5A, ATP and magnesium
Analyse Crystal structure of mycobacterium smegmatis MUTT1 in complex with AP5A, ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XD1
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudix family protein
- UniProt
- A0QUZ2
- Ligands
- 5FA, ATP, MG
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nudix family protein | protein | 292 | 33% helix, 33% strand | A0QUZ2 |
Ligands and binding sites
- 5FA · Adenosine-5'-pentaphosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 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 | 77 | 0.49 | 0.83 | 19 | GOL |
| 2 | 100 | 0.48 | 0.81 | 15 | empty |
| 3 | 101 | 0.44 | 0.78 | 21 | 5FA, MG |
Compared structures
- 5XD1 · Crystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP and magnesium · 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 5XD1 · PDBe 5XD1 · UniProt A0QUZ2
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