Research workbench
Glycogen phosphorylase complexed with 2-nitrobenzaldehyde-4-(beta-D-glucopyranosyl)-thiosemicarbazone
Analyse Glycogen phosphorylase complexed with 2-nitrobenzaldehyde-4-(beta-D-glucopyranos… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MSC
- Type
- protein
- Length
- 810 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.951
- Source
- Oryctolagus cuniculus
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- 24S
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.951 · 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
- 24S · N-({(2Z)-2-[(2-nitrophenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucopyranosylamine · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.80 | 0.96 | 33 | 24S |
| 2 | 92 | 0.72 | 0.95 | 28 | empty |
| 3 | 320 | 0.70 | 0.84 | 41 | empty |
| 4 | 226 | 0.52 | 0.76 | 20 | empty |
| 5 | 103 | 0.50 | 0.81 | 18 | empty |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 3MSC · Glycogen phosphorylase complexed with 2-nitrobenzaldehyde-4-(beta-D… · 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 3MSC · PDBe 3MSC · UniProt P00489
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