Research workbench
Crystal structure of 12-oxophytodienoate reductase 1 from tomato complexed with PEG400
Analyse Crystal structure of 12-oxophytodienoate reductase 1 from tomato complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ICP
- Type
- protein
- Length
- 716 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, SO4, CL
- Pockets
- 4 · best druggability 0.74
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 | 358 | 35% helix, 15% strand | Q9XG54 |
| B | 12-oxophytodienoate reductase 1 (EC 1.3.1.42) | protein | 358 | 37% helix, 15% strand | Q9XG54 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- 2PE · Nonaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.74 | 0.81 | 56 | SO4, FMN, 2PE |
| 2 | 688 | 0.73 | 0.79 | 59 | SO4, FMN, 2PE |
| 3 | 157 | 0.49 | 0.77 | 19 | empty |
| 4 | 88 | 0.40 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 403 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1ICP · Crystal structure of 12-oxophytodienoate reductase 1 from tomato complexed with PEG400 · 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 1ICP · PDBe 1ICP · UniProt Q9XG54
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