Research workbench
Crystal structure of human muscle glycogen phosphorylase a with AMP and glucose
Analyse Crystal structure of human muscle glycogen phosphorylase a with AMP and glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z8D
- Type
- protein
- Length
- 821 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
- P11217
- Ligands
- AMP, ADE, GLC
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 821 | 52% helix, 15% strand | P11217 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- ADE · Adenine · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.79 | 0.96 | 36 | empty |
| 2 | 137 | 0.78 | 0.96 | 33 | GLC |
| 3 | 320 | 0.62 | 0.79 | 43 | empty |
| 4 | 236 | 0.52 | 0.76 | 20 | AMP |
| 5 | 197 | 0.51 | 0.77 | 31 | empty |
Modifications
Observed in the structure: 2 modified (cofactor, phosphorylation).
Compared structures
- 1Z8D · Crystal Structure of Human Muscle Glycogen Phosphorylase a with AMP and Glucose · the same entry in another collection · chain A against A, TM-score 1.00
- P11217 · AlphaFold monomer V2.0 prediction for glycogen phosphorylase, muscle form (P11217) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P11217
- Elsewhere: RCSB PDB 1Z8D · PDBe 1Z8D · UniProt P11217
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