Research workbench
Crystal structure of the Y364F mutant of 12-oxophytodienoate reductase 3 from tomato
Analyse Crystal structure of the Y364F mutant of 12-oxophytodienoate reductase 3 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HS8
- Type
- protein
- Length
- 730 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12-oxophytodienoate reductase 3
- EC
- 1.3.1.42
- UniProt
- Q9FEW9
- Ligands
- FMN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) | protein | 367 | 40% helix, 14% strand | Q9FEW9 |
| B | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) | protein | 363 | 39% helix, 16% strand | Q9FEW9 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.74 | 0.80 | 67 | FMN |
| 2 | 478 | 0.71 | 0.80 | 41 | FMN |
| 3 | 275 | 0.64 | 0.81 | 36 | empty |
| 4 | 181 | 0.47 | 0.76 | 23 | empty |
| 5 | 63 | 0.38 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 566 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2HS8 · Crystal structure of the Y364F mutant of 12-oxophytodienoate reductase 3 from tomato · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.99
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 Q9FEW9
- Elsewhere: RCSB PDB 2HS8 · PDBe 2HS8 · UniProt Q9FEW9
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