Research workbench
Structure of the ternary complex of a zingiber officinale double bond reductase in complex with NADP and coniferyl aldehyde
Analyse Structure of the ternary complex of a zingiber officinale 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
- 4WGG
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Zingiber officinale
- Molecule
- Double Bond Reductase
- Ligands
- NAP, CIY
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double Bond Reductase | protein | 352 | 31% helix, 27% strand | — |
| B | Double Bond Reductase | protein | 346 | 32% helix, 27% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CIY · (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.82 | 0.89 | 56 | NAP, CIY |
| 2 | 833 | 0.79 | 0.82 | 85 | NAP |
| 3 | 327 | 0.61 | 0.78 | 42 | empty |
| 4 | 174 | 0.48 | 0.76 | 25 | empty |
| 5 | 143 | 0.42 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1157 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4WGG · Structure of the ternary complex of a zingiber officinale double bond reductase in… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 4WGG · PDBe 4WGG
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