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Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP
Analyse Structural mechanism for glycogen phosphorylase control by phosphorylation and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GPA
- Type
- protein
- Length
- 3,311 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase a
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glycogen phosphorylase a (EC 2.4.1.1) | protein | 828 | 49% helix, 14% strand | P00489 |
| B | Glycogen phosphorylase a (EC 2.4.1.1) | protein | 827 | 51% helix, 13% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 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 | 1096 | 0.86 | 0.86 | 99 | SO4, PLP |
| 2 | 1166 | 0.85 | 0.86 | 103 | SO4, PLP |
| 3 | 783 | 0.85 | 0.88 | 73 | SO4, PLP |
| 4 | 815 | 0.85 | 0.87 | 77 | SO4, PLP |
| 5 | 1063 | 0.83 | 0.83 | 85 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2538 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2456 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 872 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 824 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 406 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 modified (pyridoxal phosphate Schiff base, phosphorylation).
Compared structures
- 1GPA · Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP · 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 1GPA · PDBe 1GPA · UniProt P00489
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