MolNFT v1 · #49549 · protein
Glycogen phosphorylase B in complex with (1R)-3'-(4- nitrophenyl)-SPIRO[1,5-anhydro-D-glucitol-1,5'-isoxazoline]
2QRM · Glycogen phosphorylase, muscle form: “Glycogen phosphorylase B in complex with (1R)-3'-(4- nitrophenyl)-SPIRO[1,5-anhydro-D-glucitol-1,5'-isoxazolin…”. X-ray diffraction, 1 ligand (M09), 11 pockets (best druggability 0.81). MolNFT…
- PDB
- 2QRM
- Type
- protein
- Length
- 810 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
- M09
- Pockets
- 11 · best druggability 0.81
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 | 810 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- M09 · (3S,5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-(4-nitrophenyl)-1,6-dioxa-2-azaspiro[4.5]decane-8,9,10-triol · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.81 | 0.96 | 36 | M09 |
| 2 | 147 | 0.79 | 0.96 | 43 | empty |
| 3 | 293 | 0.68 | 0.83 | 39 | empty |
| 4 | 109 | 0.51 | 0.81 | 19 | empty |
| 5 | 110 | 0.51 | 0.81 | 22 | empty |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 2QRM · Glycogen Phosphorylase b in complex with (1R)-3'-(4-nitrophenyl)-spiro[1,5-anhydro-D-gluci… · 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 2QRM · PDBe 2QRM · UniProt P00489
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