MolNFT v1 · #51911 · protein
The structure of daidzin, a naturally occurring anti alcohol-addiction agent, in complex with human mitochondrial aldehyde dehydrogenase
2VLE · Aldehyde dehydrogenase, mitochondrial: “The structure of daidzin, a naturally occurring anti alcohol-addiction agent, in complex with human…”. X-ray diffraction, 1 ligand (DZN), 20 pockets (best druggability 0.90). MolNFT v1 #51911…
- PDB
- 2VLE
- Type
- protein
- Length
- 3,952 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase, mitochondrial
- EC
- 1.2.1.3
- UniProt
- P05091
- Ligands
- DZN
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 494 | 41% helix, 21% strand | P05091 |
Ligands and binding sites
- DZN · Daidzin · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.90 | 0.93 | 72 | empty |
| 2 | 891 | 0.90 | 0.93 | 71 | empty |
| 3 | 451 | 0.86 | 0.93 | 43 | empty |
| 4 | 434 | 0.85 | 0.93 | 40 | empty |
| 5 | 194 | 0.83 | 0.97 | 40 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2895 Ų buried · 48 hydrogen bonds · protein-protein
- G–H · 2890 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2872 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2870 Ų buried · 49 hydrogen bonds · protein-protein
- E–H · 1607 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2VLE · The structure of daidzin, a naturally occurring anti alcohol- addiction agent, in complex… · the same entry in another collection · chain H against H, TM-score 1.00
- P05091 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, mitochondrial (P05091) · a predicted model of the same protein · chain D 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 P05091
- Elsewhere: RCSB PDB 2VLE · PDBe 2VLE · UniProt P05091
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