Research workbench
Phosphorylase recognition and phosphorylysis of its oligosaccharide substrate: answers to a long outstanding question
Analyse Phosphorylase recognition and phosphorylysis 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
- 1QM5
- 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
- SGC, PLP, GLC, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Maltodextrin phosphorylase (EC 2.4.1.1) | protein | 796 | 54% helix, 13% strand | P00490 |
Ligands and binding sites
- SGC · 4-thio-beta-D-glucopyranose · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.84 | 0.85 | 73 | empty |
| 2 | 702 | 0.82 | 0.86 | 85 | GLC, SGC, PO4, PLP |
| 3 | 666 | 0.81 | 0.86 | 83 | GLC, SGC, PO4, PLP |
| 4 | 63 | 0.74 | 0.99 | 17 | empty |
| 5 | 54 | 0.73 | 0.99 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2149 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1QM5 · Phosphorylase recognition and phosphorylysis 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 1QM5 · PDBe 1QM5 · UniProt P00490
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