MolNFT v1 · #111556 · protein
Glycogen phosphorylase in complex with ellagic acid
4YUA · Glycogen phosphorylase, muscle form: “Glycogen phosphorylase in complex with ellagic acid”. X-ray diffraction, 2 ligands (PLP, REF), 15 pockets (best druggability 0.85). MolNFT v1 #111556 on GenesisL1: 3D structure, binding sites…
- PDB
- 4YUA
- 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
- PLP, REF
- Pockets
- 15 · 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
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- REF · 2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.85 | 0.96 | 65 | PLP |
| 2 | 86 | 0.73 | 0.95 | 25 | empty |
| 3 | 50 | 0.69 | 0.98 | 17 | empty |
| 4 | 280 | 0.69 | 0.84 | 40 | empty |
| 5 | 234 | 0.53 | 0.76 | 21 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4YUA · Glycogen phosphorylase in complex with ellagic acid · 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 4YUA · PDBe 4YUA · UniProt P00489
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