Research workbench
Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question
Analyse Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E4O
- Type
- protein
- Length
- 1,592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin phosphorylase
- EC
- 2.4.1.1
- UniProt
- P00490
- Ligands
- PLP, GLC, BGC
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Maltodextrin phosphorylase (EC 2.4.1.1) | protein | 796 | 53% helix, 11% strand | P00490 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.84 | 0.85 | 81 | empty |
| 2 | 706 | 0.82 | 0.86 | 86 | BGC, GLC, PLP |
| 3 | 714 | 0.81 | 0.85 | 88 | BGC, GLC, PLP |
| 4 | 512 | 0.67 | 0.78 | 52 | empty |
| 5 | 480 | 0.65 | 0.78 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 2083 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1E4O · Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to… · the same entry in another collection · chain A against A, TM-score 1.00
- P00490 · AlphaFold monomer V2.0 prediction for maltodextrin phosphorylase (P00490) · a predicted model of the same protein · 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 P00490
- Elsewhere: RCSB PDB 1E4O · PDBe 1E4O · UniProt P00490
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