Research workbench
Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Binary Complex
Analyse Crystal structure of Arabidopsis thaliana Double Bond Reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J3I
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- ARABIDOPSIS THALIANA
- Molecule
- NADP-dependent oxidoreductase P1
- UniProt
- Q39172
- Ligands
- NAP
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADP-dependent oxidoreductase P1 | protein | 336 | 29% helix, 25% strand | Q39172 |
| B | NADP-dependent oxidoreductase P1 | protein | 345 | 26% helix, 25% strand | Q39172 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.80 | 0.85 | 64 | NAP |
| 2 | 617 | 0.78 | 0.83 | 61 | NAP |
| 3 | 200 | 0.55 | 0.79 | 23 | empty |
| 4 | 75 | 0.30 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1399 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2J3I · Crystal structure of arabidopsis thaliana double bond reductase (AT5G16970)-binary complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q39172 · AlphaFold monomer V2.0 prediction for NADPH-dependent oxidoreductase 2-alkenal reductase… · 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 Q39172
- Elsewhere: RCSB PDB 2J3I · PDBe 2J3I · UniProt Q39172
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