MolNFT v1 · #122290 · protein
Crystal structure of human brain glycogen phosphorylase
5IKO · Glycogen phosphorylase, brain form: “Crystal structure of human brain glycogen phosphorylase”. X-ray diffraction, 2 ligands (PLP, PO4), 10 pockets (best druggability 0.78). MolNFT v1 #122290 on GenesisL1: 3D structure, binding sites…
- PDB
- 5IKO
- Type
- protein
- Length
- 807 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, PO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, brain form (EC 2.4.1.1) | protein | 807 | 54% helix, 15% strand | P11216 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- P6G · Hexaethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.78 | 0.80 | 87 | PLP |
| 2 | 66 | 0.71 | 0.97 | 24 | empty |
| 3 | 535 | 0.70 | 0.80 | 70 | empty |
| 4 | 197 | 0.51 | 0.77 | 23 | P6G |
| 5 | 103 | 0.49 | 0.81 | 27 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5IKO · Crystal structure of human brain glycogen phosphorylase · 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 5IKO · PDBe 5IKO · UniProt P11216
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