Research workbench
Crystal structure of protein kinase a in complex with the pki peptide and an amino-pyridinylbenzamide based inhibitor.
Analyse Crystal structure of protein kinase a in complex with the pki peptide and an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E99
- Type
- protein
- Length
- 351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Pki peptide
- EC
- 2.7.11.11
- UniProt
- P00517, P61925
- Ligands
- J0G
- Pockets
- 4 · best druggability 0.79
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 | 333 | 36% helix, 16% strand | P00517 |
| B | Pki peptide | protein | 18 | 39% helix, 0% strand | P61925 |
Ligands and binding sites
- J0G · 2-[(2-aminoethyl)amino]-N-[(1R)-1-(3-methoxyphenyl) ethyl]-4-(pyridin-4-yl)benzamide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.79 | 0.86 | 44 | J0G |
| 2 | 115 | 0.46 | 0.79 | 19 | empty |
| 3 | 59 | 0.32 | 0.76 | 15 | empty |
| 4 | 54 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 887 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6E99 · Crystal structure of Protein Kinase A in complex with the PKI peptide and an… · the same entry in another collection · chain A against A, 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 P61925
- Elsewhere: RCSB PDB 6E99 · PDBe 6E99 · UniProt P00517 · UniProt P61925
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