Research workbench
Glycogen phosphorylase B in complex with 28
Analyse Glycogen phosphorylase B in complex with 28 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QA8
- Type
- protein
- Length
- 806 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- HTE, PLP
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 806 | 53% helix, 16% strand | P00489 |
Ligands and binding sites
- HTE · (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-8,9, 10-tris(oxidanyl)-2-phenyl-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one · ligand · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.87 | 0.93 | 62 | HTE, PLP |
| 2 | 77 | 0.71 | 0.95 | 29 | empty |
| 3 | 340 | 0.69 | 0.83 | 38 | empty |
| 4 | 200 | 0.55 | 0.79 | 25 | empty |
| 5 | 96 | 0.51 | 0.83 | 20 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6QA8 · Glycogen Phosphorylase b in complex with 28 · 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 6QA8 · PDBe 6QA8 · UniProt P00489
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