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The 1.76 a resolution crystal structure of glycogen phosphorylase B complexed with glucose and CP320626, a potential antidiabetic drug
Analyse The 1.76 a resolution crystal structure of glycogen phosphorylase B complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H5U
- Type
- protein
- Length
- 811 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- CHI, PLP, GLC
- 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 (EC 2.4.1.1) | protein | 811 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- CHI · 5-chloro-1H-indole-2-carboxylic acid [1-(4-fluorobenzyl)-2-(4-hydroxypiperidin-1YL)-2-oxoethyl]amide · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 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 | 290 | 0.85 | 0.96 | 54 | GLC, PLP |
| 2 | 139 | 0.78 | 0.96 | 44 | empty |
| 3 | 298 | 0.70 | 0.84 | 36 | empty |
| 4 | 217 | 0.53 | 0.77 | 26 | empty |
| 5 | 112 | 0.52 | 0.82 | 18 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1H5U · The 1.76 a resolution crystal structure of glycogen phosphorylase B complexed with… · 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 1H5U · PDBe 1H5U · UniProt P00489
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