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Structure of aminoaldehyde dehydrogenase 1 from solanum lycopersium (SLAMADH1) with a thiohemiacetal intermediate
Analyse Structure of aminoaldehyde dehydrogenase 1 from solanum lycopersium (SLAMADH1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I9B
- Type
- protein
- Length
- 992 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative betaine aldehyde dehyrogenase
- UniProt
- Q56R04
- Ligands
- NAD, 1KA, NA
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative betaine aldehyde dehyrogenase | protein | 496 | 41% helix, 21% strand | Q56R04 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 1KA · (2-hydroxyethoxy)acetaldehyde · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.85 | 0.86 | 108 | empty |
| 2 | 439 | 0.72 | 0.82 | 44 | EDO, 1KA |
| 3 | 392 | 0.72 | 0.83 | 37 | PEG, 1KA |
| 4 | 351 | 0.61 | 0.77 | 42 | NAD |
| 5 | 335 | 0.60 | 0.77 | 44 | NAD |
Interfaces
1 interface between chains.
- A–B · 3987 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 4I9B · Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a… · the same entry in another collection · 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 Q56R04
- Elsewhere: RCSB PDB 4I9B · PDBe 4I9B · UniProt Q56R04
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