Research workbench
Comparison of the binding of glucose and glucose-1-phosphate derivatives to T-state glycogen phosphorylase B
Analyse Comparison of the binding of glucose and glucose-1-phosphate derivatives to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GPB
- Type
- protein
- Length
- 833 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase B
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- GFP, PLP
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase B (EC 2.4.1.1) | protein | 833 | 51% helix, 15% strand | P00489 |
Ligands and binding sites
- GFP · 2-deoxy-2-fluoro-1-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.86 | 0.95 | 52 | GFP, PLP |
| 2 | 143 | 0.77 | 0.94 | 41 | empty |
| 3 | 444 | 0.75 | 0.84 | 48 | empty |
| 4 | 142 | 0.55 | 0.81 | 25 | empty |
| 5 | 169 | 0.50 | 0.77 | 19 | GFP |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4GPB · Comparison of the binding of glucose and glucose-1-phosphate derivatives to T-state… · 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 4GPB · PDBe 4GPB · UniProt P00489
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