MolNFT v1 · #191552 · protein
The allosteric transition of glycogen phosphorylase
9GPB · Glycogen phosphorylase B: “The allosteric transition of glycogen phosphorylase”. X-ray diffraction, 2 ligands (PLP, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #191552 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 9GPB
- Type
- protein
- Length
- 3,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase B
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycogen phosphorylase B (EC 2.4.1.1) | protein | 823 | 46% helix, 14% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.83 | 0.84 | 86 | empty |
| 2 | 955 | 0.82 | 0.84 | 80 | empty |
| 3 | 180 | 0.81 | 0.96 | 42 | empty |
| 4 | 455 | 0.81 | 0.88 | 57 | SO4, PLP |
| 5 | 120 | 0.79 | 0.98 | 39 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2450 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2422 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 838 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 9GPB · The allosteric transition of glycogen phosphorylase · 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 9GPB · PDBe 9GPB · UniProt P00489
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