MolNFT v1 · #142954 · protein
Crystal structure of RNA dioxygenase bound with an inhibitor
6AKW · Alpha-ketoglutarate-dependent dioxygenase fto: “Crystal structure of RNA dioxygenase bound with an inhibitor”. X-ray diffraction, 2 ligands (AKG, 8S3), 5 pockets (best druggability 0.70). MolNFT v1 #142954 on GenesisL1: 3D…
- PDB
- 6AKW
- Type
- protein
- Length
- 434 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase fto
- EC
- 1.14.11.-
- UniProt
- Q9C0B1
- Ligands
- AKG, 8S3
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase fto (EC 1.14.11.-) | protein | 434 | 42% helix, 22% strand | Q9C0B1 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- 8S3 · 2-[[2,6-bis(chloranyl)-4-(3,5-dimethyl-1,2-oxazol-4-yl)phenyl]amino]benzoic acid · ligand · 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 | 285 | 0.70 | 0.84 | 39 | AKG, 8S3 |
| 2 | 51 | 0.70 | 0.98 | 16 | empty |
| 3 | 53 | 0.31 | 0.77 | 15 | empty |
| 4 | 55 | 0.31 | 0.76 | 13 | empty |
| 5 | 50 | 0.30 | 0.76 | 10 | empty |
Compared structures
- 6AKW · Crystal structure of RNA dioxygenase bound with an inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9C0B1 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent dioxygenase fto… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9C0B1
- Elsewhere: RCSB PDB 6AKW · PDBe 6AKW · UniProt Q9C0B1
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