MolNFT v1 · #49553 · protein
Glycogen phosphorylase B in complex with (1R)-3'-(4- methylphenyl)-SPIRO[1,5-anhydro-D-glucitol-1,5'- isoxazoline]
2QRQ · Glycogen phosphorylase, muscle form: “Glycogen phosphorylase B in complex with (1R)-3'-(4- methylphenyl)-SPIRO[1,5-anhydro-D-glucitol-1,5'…”. X-ray diffraction, 1 ligand (S13), 11 pockets (best druggability 0.84). MolNFT v1 #49553…
- PDB
- 2QRQ
- Type
- protein
- Length
- 808 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
- S13
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 808 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- S13 · (3S,5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-(4-methylphenyl)-1,6-dioxa-2-azaspiro[4.5]decane-8,9,10-triol · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 16 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.84 | 0.95 | 38 | S13 |
| 2 | 123 | 0.78 | 0.96 | 38 | empty |
| 3 | 258 | 0.69 | 0.85 | 39 | empty |
| 4 | 119 | 0.55 | 0.83 | 20 | empty |
| 5 | 193 | 0.50 | 0.76 | 18 | DMS |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 2QRQ · Glycogen Phosphorylase b in complex with (1R)-3'-(4-methylphenyl)-spiro[1,5-anhydro-D-gluc… · 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 2QRQ · PDBe 2QRQ · UniProt P00489
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