MolNFT v1 · #166421 · protein
Structure of trehalose-6-phosphate phosphatase from salmonella typhimurium in complex with trehalose
6UPD · Trehalose-phosphate phosphatase: “Structure of trehalose-6-phosphate phosphatase from salmonella typhimurium in complex with trehalose”. X-ray diffraction, 3 ligands (GLC, MG, CL), 3 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 6UPD
- Type
- protein
- Length
- 492 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trehalose-phosphate phosphatase
- EC
- 3.1.3.12
- UniProt
- E1WGG9
- Ligands
- GLC, MG, CL
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trehalose-phosphate phosphatase (EC 3.1.3.12) | protein | 246 | 37% helix, 23% strand | E1WGG9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.80 | 0.93 | 40 | GLC, CL, MG |
| 2 | 248 | 0.80 | 0.93 | 36 | GLC, MG, CL |
| 3 | 202 | 0.48 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 150 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6UPD · Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- E1WGG9 · AlphaFold monomer V2.0 prediction for trehalose-phosphate phosphatase (E1WGG9) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 E1WGG9
- Elsewhere: RCSB PDB 6UPD · PDBe 6UPD · UniProt E1WGG9
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