Research workbench
Benzaldehyde dehydrogenase, a class 3 aldehyde dehydrogenase, with bound NADP+ and benzoate adduct
Analyse Benzaldehyde dehydrogenase, a class 3 aldehyde dehydrogenase, with bound NADP+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UCD
- Type
- protein
- Length
- 870 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)-dependent benzaldehyde dehydrogenase
- EC
- 1.2.1.28, 1.2.1.7
- UniProt
- Q84DC3
- Ligands
- NAP
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD(P)-dependent benzaldehyde dehydrogenase (EC 1.2.1.28, 1.2.1.7) | protein | 435 | 46% helix, 20% strand | Q84DC3 |
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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.81 | 0.85 | 62 | empty |
| 2 | 530 | 0.67 | 0.78 | 63 | NAP |
| 3 | 424 | 0.64 | 0.78 | 56 | empty |
| 4 | 353 | 0.62 | 0.78 | 40 | NAP |
| 5 | 308 | 0.58 | 0.77 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 3082 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5UCD · Benzaldehyde Dehydrogenase, a Class 3 Aldehyde Dehydrogenase, with bound NADP+ and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q84DC3 · AlphaFold monomer V2.0 prediction for NAD(P)-dependent benzaldehyde dehydrogenase (Q84DC3) · 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 Q84DC3
- Elsewhere: RCSB PDB 5UCD · PDBe 5UCD · UniProt Q84DC3
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