MolNFT v1 · #18753 · protein
Gsk-3 beta complexed with AMP-pnp
1PYX · Glycogen synthase kinase-3 beta: “Gsk-3 beta complexed with AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 8 pockets (best druggability 0.81). MolNFT v1 #18753 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1PYX
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen synthase kinase-3 beta
- EC
- 2.7.1.37
- UniProt
- P49841
- Ligands
- ANP, MG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen synthase kinase-3 beta (EC 2.7.1.37) | protein | 343 | 36% helix, 19% strand | P49841 |
| B | Glycogen synthase kinase-3 beta (EC 2.7.1.37) | protein | 338 | 35% helix, 20% strand | P49841 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.81 | 0.83 | 69 | MG, ANP |
| 2 | 766 | 0.78 | 0.82 | 63 | MG, ANP |
| 3 | 117 | 0.68 | 0.91 | 32 | empty |
| 4 | 134 | 0.40 | 0.75 | 35 | empty |
| 5 | 69 | 0.40 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1265 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1PYX · GSK-3 Beta complexed with AMP-PNP · 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 P49841
- Elsewhere: RCSB PDB 1PYX · PDBe 1PYX · UniProt P49841
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