MolNFT v1 · #40777 · protein
Crystal structure of arabidopsis thaliana double bond reductase (AT5G16970)-ternary complex I
2J3J · NADPH-dependent oxidoreductase 2-alkenal reductase: “Crystal structure of arabidopsis thaliana double bond reductase (AT5G16970)-ternary complex I”. X-ray diffraction, 2 ligands (NAP, HC4), 5 pockets (best druggability 0.82). MolNFT…
- PDB
- 2J3J
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH-dependent oxidoreductase 2-alkenal reductase
- EC
- 1.3.1.-, 1.3.1.74
- UniProt
- Q39172
- Ligands
- NAP, HC4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH-dependent oxidoreductase 2-alkenal reductase (EC 1.3.1.-, 1.3.1.74) | protein | 336 | 25% helix, 28% strand | Q39172 |
| B | NADPH-dependent oxidoreductase 2-alkenal reductase (EC 1.3.1.-, 1.3.1.74) | protein | 345 | 24% helix, 27% strand | Q39172 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- HC4 · 4'-hydroxycinnamic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.82 | 0.87 | 66 | NAP, HC4 |
| 2 | 633 | 0.79 | 0.84 | 62 | NAP, HC4 |
| 3 | 184 | 0.56 | 0.80 | 20 | empty |
| 4 | 68 | 0.28 | 0.73 | 15 | empty |
| 5 | 55 | 0.27 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1427 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2J3J · Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Ternary… · 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 2J3J · PDBe 2J3J · UniProt Q39172
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