MolNFT v1 · #67547 · protein
Human mitochondrial aldehyde dehydrogenase asian variant, ALDH2*2, complexed with agonist alda-1
3INL · Aldehyde dehydrogenase, mitochondrial: “Human mitochondrial aldehyde dehydrogenase asian variant, ALDH2*2, complexed with agonist alda-1”. X-ray diffraction, 2 ligands (BXB, NA), 20 pockets (best druggability 0.89). MolNFT v1 #67547…
- PDB
- 3INL
- Type
- protein
- Length
- 3,954 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
- BXB, NA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 495 | 40% helix, 22% strand | P05091 |
| B, C, D, E, F, G | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 494 | 40% helix, 22% strand | P05091 |
Ligands and binding sites
- BXB · N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 31 copies · chains A, B, C, D, E, F, H, G
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 | 715 | 0.89 | 0.94 | 68 | empty |
| 2 | 692 | 0.89 | 0.93 | 84 | empty |
| 3 | 434 | 0.86 | 0.94 | 59 | empty |
| 4 | 445 | 0.86 | 0.93 | 75 | empty |
| 5 | 195 | 0.83 | 0.97 | 36 | EDO |
Interfaces
15 interfaces between chains.
- G–H · 2773 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2763 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2740 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2673 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 1618 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3INL · Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with agonist… · 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 C 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 3INL · PDBe 3INL · UniProt P05091
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