MolNFT v1 · #182388 · protein
Crystal structure of the cytosolic domain of tribolium castaneum PINK1 phosphorylated at SER205 in complex with ADP analog
7MP9 · SERINE/THREONINE-protein kinase PINK1, mitochondrial-like…: “Crystal structure of the cytosolic domain of tribolium castaneum PINK1 phosphorylated at SER205 in complex…”. X-ray diffraction, 3 ligands (AN2, MG, SO4), 5 pockets (best…
- PDB
- 7MP9
- Type
- protein
- Length
- 414 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
- AN2, MG, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PINK1, mitochondrial-like protein | protein | 414 | 42% helix, 14% strand | D6WMX4 |
Ligands and binding sites
- AN2 · Amp phosphoramidate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- PG4 · Tetraethylene glycol · additive · 3 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.66 | 0.80 | 32 | PG4 |
| 2 | 294 | 0.63 | 0.80 | 41 | MG, PG4, AN2 |
| 3 | 168 | 0.47 | 0.76 | 24 | empty |
| 4 | 96 | 0.40 | 0.77 | 16 | SO4 |
| 5 | 86 | 0.36 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7MP9 · Crystal structure of the cytosolic domain of Tribolium castaneum PINK1 phosphorylated at… · 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 D6WMX4
- Elsewhere: RCSB PDB 7MP9 · PDBe 7MP9 · UniProt D6WMX4
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