MolNFT v1 · #87088 · protein
Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2)
4BQE · Alpha-glucan phosphorylase 2,4-glucan phosphorylase: “Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2)”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.87). MolNFT v1 #87088 on GenesisL1: 3D…
- PDB
- 4BQE
- Type
- protein
- Length
- 1,649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucan phosphorylase 2,4-glucan phosphorylase
- EC
- 2.4.1.1
- UniProt
- Q9SD76
- Ligands
- PLP
- 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 2,4-glucan phosphorylase (EC 2.4.1.1) | protein | 824 | 52% helix, 15% strand | Q9SD76 |
| B | Alpha-glucan phosphorylase 2,4-glucan phosphorylase (EC 2.4.1.1) | protein | 825 | 52% helix, 15% strand | Q9SD76 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.87 | 0.88 | 80 | empty |
| 2 | 982 | 0.83 | 0.85 | 105 | PLP |
| 3 | 952 | 0.79 | 0.81 | 77 | PLP, GOL |
| 4 | 248 | 0.73 | 0.87 | 50 | empty |
| 5 | 230 | 0.72 | 0.87 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 2736 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4BQE · Arabidopsis thaliana Cytosolic Alpha-1,4-glucan Phosphorylase (PHS2) · 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 4BQE · PDBe 4BQE · UniProt Q9SD76
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