MolNFT v1 · #17729 · protein
Crystal structure of glycogen phosphorylase B in complex with beta cyclodextrin
1P2D · Glycogen phosphorylase, muscle form: “Crystal structure of glycogen phosphorylase B in complex with beta cyclodextrin”. X-ray diffraction, 2 ligands (PLP, GLC), 14 pockets (best druggability 0.84). MolNFT v1 #17729 on GenesisL1: 3D…
- PDB
- 1P2D
- 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, GLC
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 810 | 52% helix, 15% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.84 | 0.96 | 57 | PLP |
| 2 | 90 | 0.72 | 0.95 | 28 | empty |
| 3 | 51 | 0.70 | 0.98 | 17 | empty |
| 4 | 320 | 0.70 | 0.83 | 40 | empty |
| 5 | 119 | 0.54 | 0.82 | 17 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1P2D · Crystal Structure of Glycogen Phosphorylase B in complex with Beta Cyclodextrin · 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 1P2D · PDBe 1P2D · UniProt P00489
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