Research workbench
X-ray crystal structure of arabidopsis thaliana 12-oxophytodienoate reductase isoform 3 (ATOPR3) in complex with 8-iso prostaglandin A1 and its cofactor, flavin mononucleotide.
Analyse X-ray crystal structure of arabidopsis thaliana 12-oxophytodienoate reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G5W
- Type
- protein
- Length
- 729 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
- Q9FUP0
- Ligands
- FMN, 8PG
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) | protein | 363 | 37% helix, 16% strand | Q9FUP0 |
| B | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) | protein | 366 | 37% helix, 16% strand | Q9FUP0 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- 8PG · (8S,12S)-15S-hydroxy-9-oxoprosta-10Z,13E-dien-1-oic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.70 | 0.79 | 41 | FMN, 8PG |
| 2 | 469 | 0.69 | 0.79 | 43 | FMN, 8PG |
| 3 | 614 | 0.68 | 0.77 | 47 | empty |
| 4 | 74 | 0.45 | 0.81 | 14 | empty |
| 5 | 83 | 0.44 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 295 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2G5W · X-ray crystal structure of Arabidopsis thaliana 12-oxophytodienoate reductase isoform 3… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FUP0 · AlphaFold monomer V2.0 prediction for 12-oxophytodienoate reductase 3 (Q9FUP0) · a predicted model of the same protein · chain A 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 Q9FUP0
- Elsewhere: RCSB PDB 2G5W · PDBe 2G5W · UniProt Q9FUP0
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