Research workbench
Phosphorylated form of yeast glycogen phosphorylase with phosphate bound in the active site.
Analyse Phosphorylated form of yeast glycogen phosphorylase with phosphate bound in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YGP
- Type
- protein
- Length
- 1,716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeast glycogen phosphorylase
- UniProt
- P06738
- Ligands
- PLP, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Yeast glycogen phosphorylase | protein | 858 | 55% helix, 15% strand | P06738 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.85 | 0.87 | 76 | empty |
| 2 | 1105 | 0.83 | 0.84 | 124 | PO4, PLP |
| 3 | 922 | 0.82 | 0.84 | 110 | PO4, PLP |
| 4 | 124 | 0.75 | 0.94 | 41 | empty |
| 5 | 129 | 0.65 | 0.88 | 27 | PO4 |
Interfaces
1 interface between chains.
- A–B · 3536 Ų buried · 173 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1YGP · Phosphorylated form of yeast glycogen phosphorylase with phosphate bound in the active… · the same entry in another collection · chain A against A, TM-score 1.00
- P06738 · AlphaFold monomer V2.0 prediction for glycogen phosphorylase (P06738) · 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 P06738
- Elsewhere: RCSB PDB 1YGP · PDBe 1YGP · UniProt P06738
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