MolNFT v1 · #41133 · protein
The crystal structure of the kinase domain of the protein kinase C theta in complex with nvp-XAA228 at 2.32A resolution.
2JED: “The crystal structure of the kinase domain of the protein kinase C theta in complex with nvp-XAA228 at 2.32A…”. X-ray diffraction, 1 ligand (LG8), 9 pockets (best druggability 0.78). MolNFT v1 #41133 on GenesisL1: 3D structure…
- PDB
- 2JED
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase C theta
- EC
- 2.7.11.13
- UniProt
- Q04759
- Ligands
- LG8
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase C theta (EC 2.7.11.13) | protein | 326 | 37% helix, 17% strand | Q04759 |
| B | Protein kinase C theta (EC 2.7.11.13) | protein | 322 | 38% helix, 17% strand | Q04759 |
Ligands and binding sites
- LG8 · 3-(8-dimethylaminomethyl-6,7,8,9-tetrahydro-pyrido[1,2-a]indol-10-yl)-4-(1-methyl-1H-indol-3-yl)-pyrrole-2,5-dione · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.78 | 0.86 | 33 | LG8 |
| 2 | 285 | 0.69 | 0.84 | 26 | LG8 |
| 3 | 560 | 0.68 | 0.78 | 51 | empty |
| 4 | 153 | 0.52 | 0.80 | 25 | empty |
| 5 | 190 | 0.51 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 606 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 2JED · The crystal structure of the kinase domain of the protein kinase C theta in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04759 · AlphaFold monomer V2.0 prediction for protein kinase C theta type (Q04759) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q04759
- Elsewhere: RCSB PDB 2JED · PDBe 2JED · UniProt Q04759
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