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Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5- methyl-1,3,4-oxadiazole,-benzothiazole, and-benzimidazole, inhibitors of muscle glycogen phosphorylase B. evidence for a new binding site.
Analyse Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XL0
- Type
- protein
- Length
- 810 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- OX2, PLP
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 810 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- OX2 · (1R)-1,5-anhydro-1-(5-methyl-1,3,4-oxadiazol-2-yl)-D-glucitol · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.85 | 0.96 | 50 | OX2, PLP |
| 2 | 80 | 0.72 | 0.96 | 28 | empty |
| 3 | 256 | 0.68 | 0.84 | 35 | empty |
| 4 | 97 | 0.51 | 0.83 | 20 | empty |
| 5 | 219 | 0.51 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1XL0 · Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5-methyl-1,3,4-oxadiazol… · 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 1XL0 · PDBe 1XL0 · UniProt P00489
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