MolNFT v2 · #185640 · protein
C1B domain of Protein kinase C in complex with diacylglycerol-lactone (AJH-836) and 1,2-diheptanoyl-sn-glycero-3-phosphocholine
7LEO · Protein kinase C delta type: “C1B domain of Protein kinase C in complex with diacylglycerol-lactone (AJH-836) and…”. X-ray diffraction at 1.65, 3 ligands (XP5, XZJ, ZN), 2 pockets (best druggability 0.43). MolNFT v2 #185640 on…
- PDB
- 7LEO
- Type
- protein
- Length
- 102 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.65
- Source
- Rattus norvegicus
- Molecule
- Protein kinase C delta type
- UniProt
- A0A140UHX0
- Ligands
- XP5, XZJ, ZN
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · resolution 1.65 · 2 distinct chains · 12% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase C delta type | protein | 52 | 12% helix, 23% strand | A0A140UHX0 |
| D | Protein kinase C delta type | protein | 50 | 12% helix, 24% strand | A0A140UHX0 |
Ligands and binding sites
- XP5 · (4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide · ligand · 3 copies · chains A, D
- XZJ · {(2R,4E)-2-(hydroxymethyl)-4-[5-methyl-3-(2-methylpropyl)hexylidene]-5-oxooxolan-2-yl}methyl 2,2-dimethylpropanoate · ligand · chains D
- ZN · Zinc ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.43 | 0.74 | 22 | empty |
| 2 | 88 | 0.37 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–D · 263 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7LEO · C1B domain of protein kinase C in complex with diacylglycerol-lactone (ajh-836) and… · 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 7LEO · PDBe 7LEO · UniProt A0A140UHX0
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