Research workbench
Structure of rabbit muscle glycogen phosphorylase in complex with ligand
Analyse Structure of rabbit muscle glycogen phosphorylase in complex with ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GJ4
- Type
- protein
- Length
- 803 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
- PLR, 2TH, SO4
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 803 | 54% helix, 15% strand | P00489 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · chains A
- 2TH · 2-chloro-N-[(1R,2R)-1-hydroxy-2,3-dihydro-1H-inden-2-yl]-6H-thieno[2,3-b]pyrrole-5-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.86 | 0.95 | 64 | PLR |
| 2 | 137 | 0.79 | 0.96 | 41 | empty |
| 3 | 253 | 0.70 | 0.85 | 33 | empty |
| 4 | 138 | 0.57 | 0.83 | 20 | empty |
| 5 | 265 | 0.55 | 0.76 | 36 | SO4, 2TH |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2GJ4 · Structure of rabbit muscle glycogen phosphorylase in complex with ligand · 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 2GJ4 · PDBe 2GJ4 · UniProt P00489
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