MolNFT v1 · #108314 · protein
Crystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with 3- aminopropionaldehyde
4V37 · Betaine aldehyde dehydrogenase, chloroplastic: “Crystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with 3…”. X-ray diffraction, 4 ligands (0D8, NAD, AE3), 17 pockets (best druggability 0.86).…
- PDB
- 4V37
- Type
- protein
- Length
- 1,977 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
- 0D8, NAD, AE3, K
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Betaine aldehyde dehydrogenase, chloroplastic (EC 1.2.1.8) | protein | 495 | 41% helix, 21% strand | P17202 |
| B | Betaine aldehyde dehydrogenase, chloroplastic (EC 1.2.1.8) | protein | 494 | 41% helix, 21% strand | P17202 |
| D | Betaine aldehyde dehydrogenase, chloroplastic (EC 1.2.1.8) | protein | 493 | 41% helix, 21% strand | P17202 |
Ligands and binding sites
- 0D8 · 3-aminopropan-1-ol · ligand · 5 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.86 | 0.88 | 115 | PG4 |
| 2 | 542 | 0.85 | 0.91 | 68 | empty |
| 3 | 340 | 0.81 | 0.90 | 61 | NAD, 0D8, FMT, AE3 |
| 4 | 354 | 0.78 | 0.88 | 62 | NAD, 0D8, FMT |
| 5 | 195 | 0.78 | 0.92 | 41 | NAD, 0D8, FMT |
Interfaces
6 interfaces between chains.
- A–B · 3970 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3922 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 594 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 341 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 185 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4V37 · 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 4V37 · PDBe 4V37 · UniProt P17202
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