MolNFT v1 · #9971 · protein
Crystal structure of 12-oxophytodienoate reductase 1 from tomato complexed with 9R,13R-opda
1ICQ: “Crystal structure of 12-oxophytodienoate reductase 1 from tomato complexed with 9R,13R-opda”. X-ray diffraction, 2 ligands (FMN, OPD), 3 pockets (best druggability 0.71). MolNFT v1 #9971 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1ICQ
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12-oxophytodienoate reductase 1
- EC
- 1.3.1.42
- UniProt
- Q9XG54
- Ligands
- FMN, OPD
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 12-oxophytodienoate reductase 1 (EC 1.3.1.42) | protein | 353 | 37% helix, 15% strand | Q9XG54 |
| B | 12-oxophytodienoate reductase 1 (EC 1.3.1.42) | protein | 351 | 35% helix, 15% strand | Q9XG54 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- OPD · 9R,13R-12-oxophytodienoic acid · ligand · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.71 | 0.79 | 53 | FMN, OPD |
| 2 | 595 | 0.70 | 0.78 | 58 | FMN, OPD |
| 3 | 83 | 0.39 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 411 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1ICQ · Crystal structure of 12-oxophytodienoate reductase 1 from tomato complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XG54 · AlphaFold monomer V2.0 prediction for 12-oxophytodienoate reductase 1 (Q9XG54) · a predicted model of the same protein · chain B 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 Q9XG54
- Elsewhere: RCSB PDB 1ICQ · PDBe 1ICQ · UniProt Q9XG54
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