Research workbench
Allosteric inhibition of glycogen phosphorylase a by a potential antidiabetic drug
Analyse Allosteric inhibition of glycogen phosphorylase a by a potential antidiabetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AMV
- Type
- protein
- Length
- 812 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (glycogen phosphorylase)
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, BIN, GLC
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (glycogen phosphorylase) (EC 2.4.1.1) | protein | 812 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- BIN · 2,3-dicarboxy-4-(2-chloro-phenyl)-1-ethyl-5-isopropoxycarbonyl-6-methyl-pyridinium · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.84 | 0.96 | 49 | GLC, PLP |
| 2 | 87 | 0.72 | 0.95 | 26 | empty |
| 3 | 374 | 0.67 | 0.80 | 45 | empty |
| 4 | 124 | 0.54 | 0.82 | 19 | empty |
| 5 | 186 | 0.48 | 0.76 | 27 | empty |
Modifications
Observed in the structure: 1 cofactor, 1 modified (pyridoxal phosphate Schiff base, phosphorylation).
Compared structures
- 3AMV · Allosteric inhibition of glycogen phosphorylase a by a potential antidiabetic drug · the same entry in another collection · 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 P00489
- Elsewhere: RCSB PDB 3AMV · PDBe 3AMV · UniProt P00489
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