Research workbench
Structural basis for the activation of glycogen phosphorylase B by adenosine monophosphate
Analyse Structural basis for the activation of glycogen phosphorylase B by adenosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PYG
- Type
- protein
- Length
- 3,194 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
- AMP, PDP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glycogen phosphorylase B (EC 2.4.1.1) | protein | 801 | 53% helix, 15% strand | P00489 |
| B | Glycogen phosphorylase B (EC 2.4.1.1) | protein | 791 | 55% helix, 15% strand | P00489 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- PDP · Pyridoxal-5'-diphosphate · ligand · 4 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 | 1024 | 0.82 | 0.83 | 111 | PDP |
| 2 | 148 | 0.81 | 0.97 | 40 | empty |
| 3 | 133 | 0.80 | 0.98 | 41 | empty |
| 4 | 1065 | 0.80 | 0.82 | 75 | empty |
| 5 | 137 | 0.79 | 0.96 | 41 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2349 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1878 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 791 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 782 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 145 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1PYG · Structural basis for the activation of glycogen phosphorylase B by adenosine monophosphate · 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 1PYG · PDBe 1PYG · UniProt P00489
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.