MolNFT v1 · #57901 · protein
Protein kinase a sixfold mutant model of aurora B with inhibitor vx- 680
3AMB · Camp-dependent protein kinase catalytic subunit alpha: “Protein kinase a sixfold mutant model of aurora B with inhibitor vx- 680”. X-ray diffraction, 1 ligand (VX6), 4 pockets (best druggability 0.77). MolNFT v1 #57901 on GenesisL1…
- PDB
- 3AMB
- Type
- protein
- Length
- 363 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
- VX6
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% 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 | 343 | 38% helix, 16% strand | P17612 |
| B | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 30% helix, 5% strand | P61925 |
Ligands and binding sites
- VX6 · Cyclopropanecarboxylic acid {4-[4-(4-methyl-piperazin-1-yl)-6-(5-methyl-2H-pyrazol-3-ylamino)-pyrimidin-2-ylsulfanyl]-phenyl}-amide · ligand · 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 | 687 | 0.77 | 0.82 | 60 | VX6 |
| 2 | 274 | 0.60 | 0.79 | 31 | empty |
| 3 | 104 | 0.37 | 0.75 | 20 | empty |
| 4 | 55 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 3AMB · Protein kinase A sixfold mutant model of Aurora B with inhibitor VX-680 · 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 0.97
- P61925 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain B against A, TM-score 0.40
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 3AMB · PDBe 3AMB · UniProt P17612 · UniProt P61925
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