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Crystal structure of PKAB3 (PKA triple mutant V123A, L173M, Q181K) with compound 18
Analyse Crystal structure of PKAB3 (PKA triple mutant V123A, L173M, Q181K) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L9M
- Type
- protein
- Length
- 715 residues
- Chains
- 4
- 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
- L9M
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 37% 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 | 340 | 38% helix, 16% strand | P17612 |
| C | Camp-dependent protein kinase inhibitor alpha | protein | 19 | 32% helix, 0% strand | P61925 |
| B | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 338 | 37% helix, 16% strand | P17612 |
| D | Camp-dependent protein kinase inhibitor alpha | protein | 18 | 39% helix, 0% strand | P61925 |
Ligands and binding sites
- L9M · (2S)-N~1~-[5-(3-methyl-1H-indazol-5-yl)-1,3,4-thiadiazol-2-yl]-3-(4-methylphenyl)propane-1,2-diamine · ligand · 2 copies · chains A, B
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 | 398 | 0.80 | 0.89 | 45 | L9M |
| 2 | 408 | 0.78 | 0.87 | 42 | L9M |
| 3 | 96 | 0.52 | 0.83 | 14 | empty |
| 4 | 92 | 0.51 | 0.82 | 14 | empty |
| 5 | 53 | 0.32 | 0.77 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 944 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 897 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3L9M · Crystal structure of PKAB3 (pka triple mutant V123A, L173M, Q181K) with compound 18 · 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 B 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 3L9M · PDBe 3L9M · UniProt P17612 · UniProt P61925
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