Research workbench
Crystal structure of protein kinase a in complex with the pki peptide and aminobenzothiazole based inhibitors
Analyse Crystal structure of protein kinase a in complex with the pki peptide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VIB
- Type
- protein
- Length
- 327 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, Q3SX13
- Ligands
- 9D1
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 309 | 39% helix, 17% strand | P00517 |
| B | Pki peptide | protein | 18 | 39% helix, 0% strand | Q3SX13 |
Ligands and binding sites
- 9D1 · 3-({[6-(pyridin-4-yl)-1,3-benzothiazol-2-yl][2-(pyrrolidin-1-yl)ethyl]amino}methyl)phenol · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.77 | 0.86 | 43 | 9D1 |
| 2 | 75 | 0.32 | 0.74 | 15 | empty |
| 3 | 67 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 854 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5VIB · Crystal structure of Protein Kinase A in complex with the PKI peptide and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q3SX13 · 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 0.44
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 5VIB · PDBe 5VIB · UniProt P00517 · UniProt Q3SX13
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