Research workbench
Crystal structure of rabbit muscle glycogen phosphorylase in complex with 3,4-dihydro-2-quinolone
Analyse Crystal structure of rabbit muscle glycogen phosphorylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IEG
- Type
- protein
- Length
- 1,608 residues
- Chains
- 2
- 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, FRY
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 803 | 53% helix, 15% strand | P00489 |
| B | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 805 | 53% helix, 16% strand | P00489 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- FRY · (2S)-N-[(3S)-1-(2-amino-2-oxoethyl)-2-oxo-1,2,3,4-tetrahydroquinolin-3-yl]-2-chloro-2H-thieno[2,3-b]pyrrole-5-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.86 | 0.86 | 88 | FRY |
| 2 | 281 | 0.85 | 0.96 | 59 | PLR |
| 3 | 267 | 0.85 | 0.96 | 55 | PLR |
| 4 | 120 | 0.78 | 0.97 | 38 | empty |
| 5 | 79 | 0.72 | 0.96 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2236 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2IEG · Crystal structure of rabbit muscle glycogen phosphorylase in complex with… · 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 2IEG · PDBe 2IEG · UniProt P00489
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