MolNFT v1 · #16692 · protein
Structure of activated form of pkb kinase domain S474D with GSK3 peptide and AMP-pnp
1O6K · Rac-beta SERINE/THREONINE protein kinase: “Structure of activated form of pkb kinase domain S474D with GSK3 peptide and AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MN), 4 pockets (best druggability 0.83). MolNFT v1 #16692 on…
- PDB
- 1O6K
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rac-beta SERINE/THREONINE protein kinase; Glycogen synthase kinase-3 beta
- EC
- 2.7.1.-, 2.7.1.37
- UniProt
- P31751, P49841
- Ligands
- ANP, MN
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rac-beta SERINE/THREONINE protein kinase (EC 2.7.1.-) | protein | 318 | 34% helix, 17% strand | P31751 |
| C | Glycogen synthase kinase-3 beta (EC 2.7.1.37) | protein | 10 | 0% helix, 20% strand | P49841 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.83 | 0.93 | 43 | ANP, MN |
| 2 | 52 | 0.39 | 0.81 | 12 | empty |
| 3 | 69 | 0.34 | 0.76 | 17 | empty |
| 4 | 55 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–C · 779 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 1O6K · Structure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
- P31751 · AlphaFold monomer V2.0 prediction for rac-beta SERINE/THREONINE- protein kinase (P31751) · 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 P31751
- Every structure of UniProt P49841
- Elsewhere: RCSB PDB 1O6K · PDBe 1O6K · UniProt P31751 · UniProt P49841
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