Research workbench
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
- 3E8E
- Type
- protein
- Length
- 2,177 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Pki inhibitor peptide
- EC
- 2.7.11.11
- UniProt
- P00517, Q3SX13
- Ligands
- G98
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, P | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 344 | 38% helix, 15% strand | P00517 |
| G, C, F, J, N, Q | Pki inhibitor peptide | protein | 20 | 35% helix, 0% strand | Q3SX13 |
| B | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 339 | 38% helix, 15% strand | P00517 |
| I | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 348 | 39% helix, 15% strand | P00517 |
| L | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 338 | 37% helix, 15% strand | P00517 |
Ligands and binding sites
- G98 · 4-[2-(4-amino-2,5-dihydro-1,2,5-oxadiazol-3-yl)-6-{[(1S)-3-amino-1-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol · ligand · 6 copies · chains A, B, E, I, L, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.84 | 0.93 | 44 | G98 |
| 2 | 403 | 0.83 | 0.91 | 44 | G98 |
| 3 | 337 | 0.83 | 0.92 | 44 | G98 |
| 4 | 331 | 0.83 | 0.92 | 45 | G98 |
| 5 | 381 | 0.83 | 0.91 | 44 | G98 |
Interfaces
15 interfaces between chains.
- P–Q · 1101 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1094 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 1094 Ų buried · 22 hydrogen bonds · protein-protein
- L–N · 1089 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 1085 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (phosphorylation).
Compared structures
- 3E8E · Crystal structures of the kinase domain of PKA in complex with ATP-competitive inhibitors · the same entry in another collection · chain Q against Q, 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 3E8E · PDBe 3E8E · UniProt P00517 · UniProt Q3SX13
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.