Research workbench
PKA in complex with a benzothiophene fragment compound.
Analyse PKA in complex with a benzothiophene fragment compound. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BX7
- Type
- protein
- Length
- 366 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Camp-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P17612, P61925
- Ligands
- 4W1
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 346 | 37% helix, 15% strand | P17612 |
| B | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 30% helix, 5% strand | P61925 |
Ligands and binding sites
- 4W1 · 1-benzothiophen-3-ylmethanol · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.81 | 0.91 | 40 | 4W1 |
| 2 | 281 | 0.58 | 0.78 | 32 | EDO |
| 3 | 110 | 0.43 | 0.78 | 19 | empty |
| 4 | 74 | 0.34 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1082 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 5BX7 · PKA in complex with a benzothiophene fragment compound. · the same entry in another collection · chain A against A, TM-score 1.00
- P17612 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P17612
- Every structure of UniProt P61925
- Elsewhere: RCSB PDB 5BX7 · PDBe 5BX7 · UniProt P17612 · UniProt P61925
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