MolNFT v1 · #11891 · protein
Crystallographic binding study of 100 mm N-benzoyl-N'-beta-D- glucopyranosyl urea to glycogen phosphorylase B
1K06: “Crystallographic binding study of 100 mm N-benzoyl-N'-beta-D- glucopyranosyl urea to glycogen phosphorylase B”. X-ray diffraction, 2 ligands (BZD, PLP), 13 pockets (best druggability 0.86). MolNFT v1 #11891 on GenesisL1: 3D…
- PDB
- 1K06
- Type
- protein
- Length
- 807 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 · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase (EC 2.4.1.1) | protein | 807 | 53% 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.86 | 0.93 | 54 | BZD, PLP |
| 2 | 158 | 0.80 | 0.96 | 41 | empty |
| 3 | 319 | 0.69 | 0.83 | 39 | empty |
| 4 | 249 | 0.54 | 0.76 | 27 | empty |
| 5 | 123 | 0.53 | 0.82 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1K06 · Crystallographic Binding Study of 100 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 1K06 · PDBe 1K06 · UniProt P00489
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