Research workbench
OPR3 variant - R283D
Analyse OPR3 variant - R283D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8QN1
- Type
- protein
- Length
- 1,494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Solanum lycopersicum
- Molecule
- 12-oxophytodienoate reductase 3
- UniProt
- Q9FEW9
- Ligands
- FMN
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.75 · 3 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 12-oxophytodienoate reductase 3 | protein | 375 | 39% helix, 15% strand | Q9FEW9 |
| C | 12-oxophytodienoate reductase 3 | protein | 374 | 39% helix, 16% strand | Q9FEW9 |
| B | 12-oxophytodienoate reductase 3 | protein | 370 | 39% helix, 16% strand | Q9FEW9 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.84 | 0.85 | 81 | MPD, FMN |
| 2 | 1184 | 0.81 | 0.82 | 109 | MPD, FMN |
| 3 | 165 | 0.77 | 0.94 | 33 | FMN |
| 4 | 149 | 0.76 | 0.94 | 31 | FMN |
| 5 | 224 | 0.55 | 0.78 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1250 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1225 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 130 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- Q9FEW9 · AlphaFold monomer V2.0 prediction for 12-oxophytodienoate reductase 3 (Q9FEW9) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9FEW9
- Elsewhere: RCSB PDB 8QN1 · PDBe 8QN1 · UniProt Q9FEW9
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