Research workbench
Crystal Structure of the glycogen phosphorylase B / N-(beta-D-glucopyranosyl)oxamic acid complex
Analyse Crystal Structure of the glycogen phosphorylase B /… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F3P
- Type
- protein
- Length
- 810 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Oryctolagus cuniculus
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, 4GP
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.94 · 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
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- 4GP · N-(carboxycarbonyl)-beta-D-glucopyranosylamine · sugar · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.85 | 0.96 | 49 | PLP, 4GP |
| 2 | 75 | 0.71 | 0.95 | 28 | empty |
| 3 | 274 | 0.69 | 0.84 | 37 | empty |
| 4 | 110 | 0.51 | 0.81 | 17 | empty |
| 5 | 196 | 0.51 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2F3P · Crystal structure of the glycogen phosphorylase B / N-(beta-D- GLUCOPYRANOSYL)OXAMIC acid… · 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 0.98
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 2F3P · PDBe 2F3P · UniProt P00489
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