MolNFT v1 · #168822 · protein
Crystal structure of a betaine aldehyde dehydrogenase from burkholderia pseudomallei bound to cofactor NAD
6WSB · NAD/NADP-dependent betaine aldehyde dehydrogenase: “Crystal structure of a betaine aldehyde dehydrogenase from burkholderia pseudomallei bound to cofactor NAD”. X-ray diffraction, 1 ligand (NAD), 7 pockets (best druggability 0.81).…
- PDB
- 6WSB
- Type
- protein
- Length
- 978 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD/NADP-dependent betaine aldehyde dehydrogenase
- EC
- 1.2.1.8
- UniProt
- Q3JLL8
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD/NADP-dependent betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 489 | 43% helix, 22% strand | Q3JLL8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.81 | 0.82 | 127 | empty |
| 2 | 411 | 0.74 | 0.84 | 40 | empty |
| 3 | 431 | 0.74 | 0.84 | 42 | empty |
| 4 | 332 | 0.58 | 0.76 | 41 | NAD |
| 5 | 217 | 0.53 | 0.77 | 33 | NAD |
Interfaces
1 interface between chains.
- A–B · 3413 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6WSB · Crystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei… · the same entry in another collection · chain A against A, TM-score 1.00
- Q3JLL8 · AlphaFold monomer V2.0 prediction for betaine aldehyde dehydrogenase (Q3JLL8) · 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 Q3JLL8
- Elsewhere: RCSB PDB 6WSB · PDBe 6WSB · UniProt Q3JLL8
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