MolNFT v1 · #121700 · protein
Structure of the human mitochondrial kinase COQ8A R611K with amppnp (cerebellar ataxia and ubiquinone deficiency through loss of unorthodox kinase activity)
5I35 · Atypical kinase ADCK3, mitochondrial: “Structure of the human mitochondrial kinase COQ8A R611K with amppnp (cerebellar ataxia and ubiquinone…”. X-ray diffraction, 1 ligand (ANP), 6 pockets (best druggability 0.82). MolNFT v1 #121700…
- 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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