MolNFT v1 · #114330 · protein
Crystal structure of aad-1 in complex with (R)-cyhalofop, MN(II), and 2-oxoglutarate
5BKD · (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase: “Crystal structure of aad-1 in complex with (R)-cyhalofop, MN(II), and 2-oxoglutarate”. X-ray diffraction, 4 ligands (AKG, RCF, MN), 7 pockets (best druggability 0.77). MolNFT…
- PDB
- 5BKD
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase
- EC
- 1.14.11.44
- UniProt
- P83310
- Ligands
- AKG, RCF, MN, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44) | protein | 289 | 25% helix, 28% strand | P83310 |
| B | (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44) | protein | 267 | 22% helix, 29% strand | P83310 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- RCF · (2R)-2-[4-(4-cyano-2-fluorophenoxy)phenoxy]propanoic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.77 | 0.91 | 38 | MN, AKG, RCF |
| 2 | 252 | 0.69 | 0.84 | 34 | MN, AKG, RCF |
| 3 | 329 | 0.60 | 0.77 | 33 | SO4 |
| 4 | 324 | 0.58 | 0.77 | 36 | empty |
| 5 | 97 | 0.48 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1038 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5BKD · Crystal structure of AAD-1 in complex with (R)-cyhalofop, Mn(II), and 2-oxoglutarate · the same entry in another collection · chain A against A, TM-score 1.00
- P83310 · AlphaFold monomer V2.0 prediction for (R)-PHENOXYPROPIONATE/ALPHA… · a predicted model of the same protein · chain B 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 P83310
- Elsewhere: RCSB PDB 5BKD · PDBe 5BKD · UniProt P83310
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