MolNFT v1 · #28518 · protein
Phosphorylated form of yeast glycogen phosphorylase with phosphate bound in the active site.
1YGP: “Phosphorylated form of yeast glycogen phosphorylase with phosphate bound in the active site.”. X-ray diffraction, 2 ligands (PLP, PO4), 20 pockets (best druggability 0.85). MolNFT v1 #28518 on GenesisL1: 3D structure, binding sites…
- 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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