MolNFT v1 · #119823 · protein
Crystal structure of mycobacterium smegmatis MUTT1 in complex with phosphate and magnesium ions (excess magnesium, II)
5GGD · Hydrolase, nudix family protein: “Crystal structure of mycobacterium smegmatis MUTT1 in complex with phosphate and magnesium ions (excess…”. X-ray diffraction, 2 ligands (MG, PO4), 6 pockets (best druggability 0.50). MolNFT v1…
- PDB
- 5GGD
- 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
- MG, PO4
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hydrolase, nudix family protein | protein | 289 | 33% helix, 34% strand | A0QUZ2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 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 | 17 | empty |
| 2 | 67 | 0.47 | 0.84 | 15 | empty |
| 3 | 80 | 0.45 | 0.81 | 17 | empty |
| 4 | 59 | 0.44 | 0.83 | 13 | empty |
| 5 | 103 | 0.41 | 0.76 | 21 | PO4, MG |
Compared structures
- 5GGD · Crystal structure of Mycobacterium smegmatis MutT1 in complex with phosphate and… · 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 5GGD · PDBe 5GGD · UniProt A0QUZ2
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