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The crystal structure of glycogen phosphorylase in complex with 14
Analyse The crystal structure of glycogen phosphorylase in complex with 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S52
- Type
- protein
- Length
- 810 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
- KVN, PLP
- Pockets
- 11 · best druggability 0.85
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 | 810 | 53% helix, 16% strand | P00489 |
Ligands and binding sites
- KVN · (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(5-phenyl-1,2,3,4-tetrazol-2-yl)oxane-3,4,5-triol · 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.85 | 0.96 | 49 | KVN, PLP |
| 2 | 78 | 0.73 | 0.96 | 26 | empty |
| 3 | 422 | 0.68 | 0.80 | 60 | empty |
| 4 | 128 | 0.54 | 0.82 | 19 | empty |
| 5 | 196 | 0.51 | 0.77 | 24 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6S52 · The crystal structure of glycogen phosphorylase in complex with 14 · 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 6S52 · PDBe 6S52 · UniProt P00489
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