Research workbench
Crystal structure of dioxygenase for auxin oxidation (dao) in rice
Analyse Crystal structure of dioxygenase for auxin oxidation (dao) in rice in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KUN
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate-dependent dioxygenase dao
- EC
- 1.14.11.-
- UniProt
- Q01IX6
- Ligands
- AKG, IAC
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxoglutarate-dependent dioxygenase dao (EC 1.14.11.-) | protein | 294 | 34% helix, 24% strand | Q01IX6 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- IAC · 1H-indol-3-ylacetic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.81 | 0.82 | 126 | AKG, IAC, GOL |
| 2 | 73 | 0.63 | 0.91 | 23 | empty |
| 3 | 57 | 0.63 | 0.93 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 810 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6KUN · Crystal structure of dioxygenase for auxin oxidation (DAO) in rice · the same entry in another collection · chain A against A, TM-score 1.00
- Q01IX6 · AlphaFold monomer V2.0 prediction for 2-oxoglutarate-dependent dioxygenase dao (Q01IX6) · 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 Q01IX6
- Elsewhere: RCSB PDB 6KUN · PDBe 6KUN · UniProt Q01IX6
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