MolNFT v1 · #87092 · protein
Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with maltotriose
4BQI · Alpha-glucan phosphorylase 2, cytosolic: “Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with maltotriose”. X-ray diffraction, 2 ligands (PLP, GLC), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 4BQI
- Type
- protein
- Length
- 1,648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucan phosphorylase 2, cytosolic
- EC
- 2.4.1.1
- UniProt
- Q9SD76
- Ligands
- PLP, GLC
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-glucan phosphorylase 2, cytosolic (EC 2.4.1.1) | protein | 824 | 51% helix, 15% strand | Q9SD76 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.86 | 0.87 | 78 | empty |
| 2 | 1002 | 0.83 | 0.84 | 116 | PLP |
| 3 | 1039 | 0.83 | 0.84 | 122 | PLP |
| 4 | 126 | 0.79 | 0.97 | 34 | empty |
| 5 | 138 | 0.79 | 0.96 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2700 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4BQI · ARABIDOPSIS THALIANA cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SD76 · AlphaFold monomer V2.0 prediction for alpha-glucan phosphorylase 2, cytosolic (Q9SD76) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9SD76
- Elsewhere: RCSB PDB 4BQI · PDBe 4BQI · UniProt Q9SD76
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