Research workbench
Crystal structure of the cytosolic domain of tribolium castaneum PINK1 phosphorylated at SER205 in complex with ADP analog
Analyse Crystal structure of the cytosolic domain of tribolium castaneum PINK1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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