MolNFT v1 · #155080 · protein
ATDAO1(DIOXYGENASE for auxin oxidation 1 from arabidopsis thaliana) - 2-oxoglutarate binray complex
6KWB · 2-oxoglutarate (2OG) and FE(II)-dependent oxygenase…: “ATDAO1(DIOXYGENASE for auxin oxidation 1 from arabidopsis thaliana) - 2-oxoglutarate binray complex”. X-ray diffraction, 2 ligands (AKG, MG), 9 pockets (best druggability 0.77).…
- PDB
- 6KWB
- Type
- protein
- Length
- 763 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate (2OG) and FE(II)-dependent oxygenase superfamily protein
- UniProt
- Q9XI75
- Ligands
- AKG, MG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoglutarate (2OG) and FE(II)-dependent oxygenase superfamily protein | protein | 267 | 30% helix, 23% strand | Q9XI75 |
| B | 2-oxoglutarate (2OG) and FE(II)-dependent oxygenase superfamily protein | protein | 266 | 30% helix, 23% strand | Q9XI75 |
| C | 2-oxoglutarate (2OG) and FE(II)-dependent oxygenase superfamily protein | protein | 230 | 34% helix, 18% strand | Q9XI75 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.77 | 0.98 | 26 | MG |
| 2 | 828 | 0.76 | 0.80 | 79 | MG, AKG |
| 3 | 446 | 0.71 | 0.81 | 60 | empty |
| 4 | 502 | 0.62 | 0.75 | 48 | empty |
| 5 | 77 | 0.55 | 0.87 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 673 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 376 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6KWB · AtDAO1(dioxygenase for auxin oxidation 1 from Arabidopsis thaliana) - 2-oxoglutarate… · 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 Q9XI75
- Elsewhere: RCSB PDB 6KWB · PDBe 6KWB · UniProt Q9XI75
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