Research workbench
Crystal structure of human brain glycogen phosphorylase bound to AMP
Analyse Crystal structure of human brain glycogen phosphorylase bound to AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IKP
- Type
- protein
- Length
- 806 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, brain form
- EC
- 2.4.1.1
- UniProt
- P11216
- Ligands
- PLP, AMP
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, brain form (EC 2.4.1.1) | protein | 806 | 52% helix, 15% strand | P11216 |
Ligands and binding sites
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 | 770 | 0.77 | 0.81 | 71 | PLP |
| 2 | 115 | 0.76 | 0.96 | 36 | empty |
| 3 | 224 | 0.64 | 0.83 | 26 | empty |
| 4 | 112 | 0.52 | 0.81 | 23 | empty |
| 5 | 200 | 0.52 | 0.77 | 24 | AMP |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5IKP · Crystal structure of human brain glycogen phosphorylase bound to AMP · the same entry in another collection · chain A against A, TM-score 1.00
- P11216 · AlphaFold monomer V2.0 prediction for glycogen phosphorylase, brain form (P11216) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P11216
- Elsewhere: RCSB PDB 5IKP · PDBe 5IKP · UniProt P11216
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