MolNFT v2 · #26636 · protein
Crystallographic studies on acyl ureas, a new class of inhibitors of glycogenphosphorylase. Broad specificity of the allosteric site
1WV1 · Glycogen phosphorylase, muscle form: “Crystallographic studies on acyl ureas, a new class of inhibitors of glycogenphosphorylase. Broad specificity…”. X-ray diffraction at 2.26, 2 ligands (PLP, BN5), 13 pockets (best druggability…
- PDB
- 1WV1
- Type
- protein
- Length
- 816 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.26
- Source
- Oryctolagus cuniculus
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, BN5
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.26 · 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 | 816 | 52% helix, 15% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- BN5 · 5-[3-({[(2,4-dichlorobenzoyl)amino]carbonyl}amino)-2-methylphenoxy]pentanoic acid · ligand · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.84 | 0.96 | 50 | PLP |
| 2 | 140 | 0.79 | 0.96 | 43 | empty |
| 3 | 292 | 0.69 | 0.84 | 32 | empty |
| 4 | 165 | 0.52 | 0.79 | 25 | empty |
| 5 | 113 | 0.52 | 0.82 | 20 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1WV1 · Crystallographic studies on acyl ureas, a new class of inhibitors of… · the same entry in another collection · chain A against A, TM-score 1.00
- P00489 · AlphaFold monomer V2.0 prediction for glycogen phosphorylase, muscle form (P00489) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 1WV1 · PDBe 1WV1 · UniProt P00489
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