Research workbench
Structure of the human mitochondrial kinase COQ8A R611K with amppnp (cerebellar ataxia and ubiquinone deficiency through loss of unorthodox kinase activity)
Analyse Structure of the human mitochondrial kinase COQ8A R611K with amppnp (cerebellar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I35
- Type
- protein
- Length
- 384 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atypical kinase ADCK3, mitochondrial
- EC
- 2.7.-.-
- UniProt
- Q8NI60
- Ligands
- ANP
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atypical kinase ADCK3, mitochondrial (EC 2.7.-.-) | protein | 384 | 54% helix, 13% strand | Q8NI60 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.82 | 0.84 | 86 | ANP |
| 2 | 122 | 0.68 | 0.89 | 22 | empty |
| 3 | 120 | 0.55 | 0.83 | 25 | empty |
| 4 | 67 | 0.44 | 0.83 | 16 | empty |
| 5 | 53 | 0.38 | 0.80 | 12 | empty |
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 5I35 · Structure of the Human mitochondrial kinase COQ8A R611K with AMPPNP (Cerebellar Ataxia… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NI60 · AlphaFold monomer V2.0 prediction for atypical kinase COQ8A, mitochondrial (Q8NI60) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q8NI60
- Elsewhere: RCSB PDB 5I35 · PDBe 5I35 · UniProt Q8NI60
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