MolNFT v1 · #87089 · protein
Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with acarbose
4BQF · Alpha-glucan phosphorylase 2, cytosolic: “Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with acarbose”. X-ray diffraction, 4 ligands (AC1, PLP, GLC), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 4BQF
- Type
- protein
- Length
- 1,651 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
- AC1, PLP, GLC, BGC
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucan phosphorylase 2, cytosolic (EC 2.4.1.1) | protein | 824 | 52% helix, 15% strand | Q9SD76 |
| B | Alpha-glucan phosphorylase 2, cytosolic (EC 2.4.1.1) | protein | 827 | 52% helix, 15% strand | Q9SD76 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A, B
- BGC · beta-D-glucopyranose · ion · 2 copies · chains B
- 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 | 1035 | 0.87 | 0.88 | 76 | empty |
| 2 | 1161 | 0.82 | 0.83 | 113 | PLP, GLC |
| 3 | 961 | 0.80 | 0.81 | 90 | PLP, GLC |
| 4 | 280 | 0.74 | 0.87 | 54 | empty |
| 5 | 272 | 0.73 | 0.87 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 2720 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4BQF · 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 4BQF · PDBe 4BQF · UniProt Q9SD76
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