Research workbench
Binding of beta-D-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase B: kinetic and crystallographic studies
Analyse Binding of beta-D-glucopyranosyl bismethoxyphosphoramidate to glycogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XC7
- 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
- GL6, PLP, SO4
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 810 | 52% helix, 15% strand | P00489 |
Ligands and binding sites
- GL6 · N-(dimethoxyphosphoryl)-beta-D-glucopyranosylamine · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.84 | 0.95 | 41 | GL6, PLP |
| 2 | 145 | 0.79 | 0.96 | 40 | empty |
| 3 | 434 | 0.68 | 0.80 | 61 | empty |
| 4 | 197 | 0.53 | 0.78 | 25 | SO4 |
| 5 | 122 | 0.53 | 0.81 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1XC7 · Binding of beta-D-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b… · 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 1XC7 · PDBe 1XC7 · UniProt P00489
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.