Research workbench
The glycogen phosphorylase B R state- AMP complex
Analyse The glycogen phosphorylase B R state- AMP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E3N
- Type
- protein
- Length
- 6,490 residues
- Chains
- 8
- 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
- AMP, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 814 | 52% helix, 14% strand | P00489 |
| B | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 815 | 51% helix, 14% strand | P00489 |
| C | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 802 | 52% helix, 14% strand | P00489 |
| D | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 815 | 51% helix, 14% strand | P00489 |
| E | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 803 | 52% helix, 14% strand | P00489 |
| F | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 813 | 50% helix, 14% strand | P00489 |
| H | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 814 | 52% helix, 14% strand | P00489 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H
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 | 1013 | 0.84 | 0.85 | 75 | empty |
| 2 | 1049 | 0.83 | 0.85 | 78 | empty |
| 3 | 917 | 0.82 | 0.84 | 78 | empty |
| 4 | 873 | 0.82 | 0.84 | 73 | empty |
| 5 | 150 | 0.80 | 0.96 | 40 | empty |
Interfaces
15 interfaces between chains.
- G–H · 2938 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2924 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2787 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2758 Ų buried · 35 hydrogen bonds · protein-protein
- E–H · 926 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (cofactor).
Compared structures
- 3E3N · The Glycogen phosphorylase b R state- AMP complex · 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 3E3N · PDBe 3E3N · UniProt P00489
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