Research workbench
C1B domain of protein kinase C in complex with diacylglycerol and dodecyl 2-(TRIMETHYLAMMONIO)ETHYL phosphate
Analyse C1B domain of protein kinase C in complex with diacylglycerol and dodecyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L92
- Type
- protein
- Length
- 414 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase C delta type
- EC
- 2.7.11.13
- UniProt
- A0A140UHX0
- Ligands
- DGA, DPV, ZN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, M, P, S, V | Protein kinase C delta type (EC 2.7.11.13) | protein | 52 | 12% helix, 23% strand | A0A140UHX0 |
| D, J | Protein kinase C delta type (EC 2.7.11.13) | protein | 51 | 6% helix, 18% strand | A0A140UHX0 |
Ligands and binding sites
- DGA · Diacyl glycerol · ligand · 10 copies · chains A, G, D, J, M, P, S, V
- DPV · dodecyl 2-(trimethylammonio)ethyl phosphate · ligand · 6 copies · chains A, D, G, J, M, P, V, S
- ZN · Zinc ion · metal · 16 copies · chains A, D, G, J, M, P, S, V
- EOH · Ethanol · additive · 2 copies · chains A, D, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.76 | 0.80 | 79 | DPV |
| 2 | 478 | 0.70 | 0.80 | 57 | empty |
| 3 | 376 | 0.68 | 0.81 | 40 | empty |
| 4 | 81 | 0.33 | 0.74 | 17 | EOH |
| 5 | 56 | 0.30 | 0.75 | 12 | empty |
Interfaces
12 interfaces between chains.
- P–S · 333 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 325 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 298 Ų buried · 9 hydrogen bonds · protein-protein
- P–V · 286 Ų buried · 8 hydrogen bonds · protein-protein
- J–M · 283 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7L92 · C1B domain of Protein kinase C in complex with diacylglycerol and dodecyl… · 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 A0A140UHX0
- Elsewhere: RCSB PDB 7L92 · PDBe 7L92 · UniProt A0A140UHX0
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