Research workbench
Structure of a peptide-substrate bound to pkciota core kinase domain
Analyse Structure of a peptide-substrate 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
- 5LIH
- Type
- protein
- Length
- 669 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase C iota type; PKC epsilon pseudo substrate sequence
- EC
- 2.7.11.13
- UniProt
- P41743
- Ligands
- AF3, ADP, MN, SCN
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase C iota type (EC 2.7.11.13) | protein | 326 | 31% helix, 16% strand | P41743 |
| B | Protein kinase C iota type (EC 2.7.11.13) | protein | 320 | 33% helix, 17% strand | P41743 |
| F | PKC epsilon pseudo substrate sequence | protein | 13 | 0% helix, 15% strand | — |
| G | PKC epsilon pseudo substrate sequence | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- AF3 · Aluminum fluoride · ligand · 4 copies · chains A, F, B, G
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, F, B, G
- MN · Manganese (II) ion · metal · 5 copies · chains A, F, B, G
- SCN · Thiocyanate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.80 | 0.92 | 41 | ADP, MN, AF3 |
| 2 | 376 | 0.78 | 0.88 | 56 | ADP, MN, AF3 |
| 3 | 68 | 0.45 | 0.82 | 18 | empty |
| 4 | 155 | 0.44 | 0.75 | 27 | empty |
| 5 | 65 | 0.43 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–F · 905 Ų buried · 12 hydrogen bonds · protein-protein
- B–G · 799 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 154 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 5LIH · Structure of a peptide-substrate 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 B 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 P41743
- Elsewhere: RCSB PDB 5LIH · PDBe 5LIH · UniProt P41743
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.