Research workbench
Structure of a PAR3-inhibitory peptide bound to pkciota core kinase domain
Analyse Structure of a PAR3-inhibitory peptide bound to pkciota core kinase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LI1
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase C iota type; Par-3 partitioning defective 3 homolog (C. elegans)
- EC
- 2.7.11.13
- UniProt
- P41743, Q28E03
- Ligands
- ANP, MG, K
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase C iota type (EC 2.7.11.13) | protein | 334 | 38% helix, 16% strand | P41743 |
| B | Par-3 partitioning defective 3 homolog (C. elegans) | protein | 20 | 0% helix, 10% strand | Q28E03 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.83 | 0.96 | 36 | ANP, MG |
| 2 | 69 | 0.47 | 0.83 | 15 | GOL |
| 3 | 127 | 0.44 | 0.76 | 25 | empty |
| 4 | 62 | 0.35 | 0.78 | 15 | empty |
| 5 | 56 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1379 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 5LI1 · Structure of a Par3-inhibitory peptide bound to PKCiota core kinase domain · the same entry in another collection · chain A against A, TM-score 1.00
- P41743 · AlphaFold monomer V2.0 prediction for protein kinase C iota type (P41743) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P41743
- Every structure of UniProt Q28E03
- Elsewhere: RCSB PDB 5LI1 · PDBe 5LI1 · UniProt P41743 · UniProt Q28E03
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