Research workbench
Crystal structure of betaine aldehyde dehydrogenase from spinach in complex with NAD
Analyse Crystal structure of betaine aldehyde dehydrogenase from spinach in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A0M
- Type
- protein
- Length
- 1,976 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
- NAD, K
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Betaine aldehyde dehydrogenase, chloroplastic (EC 1.2.1.8) | protein | 494 | 40% helix, 19% strand | P17202 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, D, C
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.86 | 0.88 | 110 | K |
| 2 | 526 | 0.85 | 0.91 | 56 | K, GOL |
| 3 | 532 | 0.83 | 0.89 | 75 | NAD |
| 4 | 482 | 0.76 | 0.84 | 65 | NAD, GOL |
| 5 | 178 | 0.76 | 0.92 | 41 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 3923 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3891 Ų buried · 54 hydrogen bonds · protein-protein
- A–D · 552 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 224 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4A0M · Crystal structure of betaine aldehyde dehydrogenase from spinach in complex with NAD · 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 B 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 4A0M · PDBe 4A0M · UniProt P17202
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