Research workbench
Crystal structure of tribolium castaneum PINK1 kinase domain in complex with AMP-pnp
Analyse Crystal structure of tribolium castaneum PINK1 kinase domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YJ9
- Type
- protein
- Length
- 343 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PINK1, mitochondrial-like protein
- UniProt
- D6WMX4
- Ligands
- ANP, MG
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | SERINE/THREONINE-protein kinase PINK1, mitochondrial-like protein | protein | 343 | 36% helix, 15% strand | D6WMX4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains D
- MG · Magnesium ion · metal · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.60 | 0.77 | 44 | ANP, MG |
| 2 | 68 | 0.31 | 0.74 | 16 | empty |
| 3 | 64 | 0.29 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5YJ9 · Crystal structure of Tribolium castaneum PINK1 kinase domain in complex with AMP-PNP · the same entry in another collection · chain D against D, 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 D6WMX4
- Elsewhere: RCSB PDB 5YJ9 · PDBe 5YJ9 · UniProt D6WMX4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.