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Crystal structures of the kinase domain of PKA in complex with ATP- competitive inhibitors
Analyse Crystal structures of the kinase domain of PKA in complex with ATP- competitive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E8C
- Type
- protein
- Length
- 2,180 residues
- Chains
- 12
- 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
- P00517, Q3SX13
- Ligands
- G96
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 344 | 38% helix, 15% strand | P00517 |
| B, D | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 347 | 37% helix, 15% strand | P00517 |
| E | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 338 | 37% helix, 16% strand | P00517 |
| G | Camp-dependent protein kinase inhibitor peptide | protein | 18 | 39% helix, 0% strand | Q3SX13 |
| H, I, K | Camp-dependent protein kinase inhibitor peptide | protein | 20 | 35% helix, 5% strand | Q3SX13 |
| J | Camp-dependent protein kinase inhibitor peptide | protein | 19 | 37% helix, 0% strand | Q3SX13 |
| L | Camp-dependent protein kinase inhibitor peptide | protein | 19 | 21% helix, 0% strand | Q3SX13 |
Ligands and binding sites
- G96 · 4-[2-(4-amino-1,2,5-oxadiazol-3-yl)-6-{[(2R)-2-amino-3-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol · ligand · 6 copies · chains A, G, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.82 | 0.92 | 45 | G96 |
| 2 | 412 | 0.81 | 0.90 | 46 | G96 |
| 3 | 448 | 0.81 | 0.88 | 50 | G96 |
| 4 | 471 | 0.80 | 0.87 | 51 | G96 |
| 5 | 463 | 0.79 | 0.87 | 51 | G96 |
Interfaces
16 interfaces between chains.
- C–I · 1055 Ų buried · 15 hydrogen bonds · protein-protein
- F–L · 1005 Ų buried · 15 hydrogen bonds · protein-protein
- E–K · 968 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 948 Ų buried · 15 hydrogen bonds · protein-protein
- D–J · 933 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (phosphorylation).
Compared structures
- 3E8C · Crystal structures of the kinase domain of PKA in complex with ATP-competitive inhibitors · the same entry in another collection · chain L against L, 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 P00517
- Every structure of UniProt Q3SX13
- Elsewhere: RCSB PDB 3E8C · PDBe 3E8C · UniProt P00517 · UniProt Q3SX13
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