Research workbench
Crystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with betaine aldehyde
Analyse Crystal structure of betaine aldehyde dehydrogenase from spinach showing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A2D
- Type
- protein
- Length
- 1,971 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betaine aldehyde dehydrogenase, chloroplastic
- EC
- 1.2.1.8
- UniProt
- P17202
- Ligands
- CHT, ETX, AE3, K
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Betaine aldehyde dehydrogenase, chloroplastic (EC 1.2.1.8) | protein | 493 | 42% helix, 21% strand | P17202 |
| C | Betaine aldehyde dehydrogenase, chloroplastic (EC 1.2.1.8) | protein | 492 | 39% helix, 21% strand | P17202 |
Ligands and binding sites
- CHT · Choline ion · ligand · 2 copies · chains A, B
- ETX · 2-ethoxyethanol · ligand · 2 copies · chains A, D
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · chains C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains A, B
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.86 | 0.90 | 91 | empty |
| 2 | 1065 | 0.85 | 0.86 | 113 | PG4 |
| 3 | 384 | 0.77 | 0.87 | 55 | empty |
| 4 | 327 | 0.74 | 0.85 | 35 | empty |
| 5 | 245 | 0.70 | 0.85 | 30 | CHT |
Interfaces
6 interfaces between chains.
- A–B · 3965 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3860 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 397 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 130 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified, 2 covalent (oxidation, covalent ligand).
Compared structures
- 5A2D · Crystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal… · the same entry in another collection · chain D against D, TM-score 1.00
- P17202 · AlphaFold monomer V2.0 prediction for betaine aldehyde dehydrogenase, chloroplastic… · 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 P17202
- Elsewhere: RCSB PDB 5A2D · PDBe 5A2D · UniProt P17202
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