MolNFT v1 · #139348 · protein
Crystal structure of mycobacterium smegmatis MUTT1 in complex with AP5A, ATP and manganese
5XD2 · Nudix family protein: “Crystal structure of mycobacterium smegmatis MUTT1 in complex with AP5A, ATP and manganese”. X-ray diffraction, 3 ligands (5FA, ATP, MN), 3 pockets (best druggability 0.50). MolNFT v1 #139348 on GenesisL1: 3D…
- PDB
- 5XD2
- 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, MN
- Pockets
- 3 · best druggability 0.50
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
- MN · Manganese (II) 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.50 | 0.82 | 14 | empty |
| 2 | 72 | 0.49 | 0.84 | 18 | GOL |
| 3 | 110 | 0.45 | 0.78 | 22 | 5FA, MN |
Compared structures
- 5XD2 · Crystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP and manganese · 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 5XD2 · PDBe 5XD2 · UniProt A0QUZ2
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