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Crystallographic binding study of 10 mm N-benzoyl-N'-beta-D- glucopyranosyl urea to glycogen phosphorylase B
Analyse Crystallographic binding study of 10 mm N-benzoyl-N'-beta-D- glucopyranosyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K08
- Type
- protein
- Length
- 817 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
- BZD, PLP
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase (EC 2.4.1.1) | protein | 817 | 52% helix, 15% strand | P00489 |
Ligands and binding sites
- BZD · N-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine · ligand · 2 copies · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.86 | 0.93 | 64 | BZD, PLP |
| 2 | 151 | 0.80 | 0.96 | 40 | empty |
| 3 | 298 | 0.70 | 0.84 | 35 | empty |
| 4 | 265 | 0.55 | 0.77 | 29 | empty |
| 5 | 116 | 0.53 | 0.82 | 18 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1K08 · Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to… · 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 1K08 · PDBe 1K08 · UniProt P00489
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