Research workbench
Binding of glucopyranosylidene-spiro-thiohydantoin to glycogen phosphorylase B: kinetic and crystallographic stud
Analyse Binding of glucopyranosylidene-spiro-thiohydantoin to 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
- 1HLF
- Type
- protein
- Length
- 830 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, GL4
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase (EC 2.4.1.1) | protein | 830 | 51% helix, 15% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- GL4 · (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-2-thioxo-6-oxa-1,3-diazaspiro[4.5]decan-4-one · ligand · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.85 | 0.95 | 53 | PLP, GL4 |
| 2 | 94 | 0.73 | 0.95 | 28 | empty |
| 3 | 66 | 0.72 | 0.97 | 20 | empty |
| 4 | 296 | 0.70 | 0.84 | 33 | empty |
| 5 | 181 | 0.54 | 0.79 | 24 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1HLF · Binding of glucopyranosylidene-spiro-thiohydantoin to glycogen phosphorylase B: kinetic… · 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 1HLF · PDBe 1HLF · UniProt P00489
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