Research workbench
Human mitochondrial aldehyde dehydrogenase asian variant, ALDH2*2, complexed with NAD+
Analyse Human mitochondrial aldehyde dehydrogenase asian variant, ALDH2*2, complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ONM
- Type
- protein
- Length
- 5,928 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase, mitochondrial precursor
- EC
- 1.2.1.3
- UniProt
- P05091
- Ligands
- GAI, ADP, NAD, NA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3) | protein | 494 | 40% helix, 22% strand | P05091 |
Ligands and binding sites
- GAI · Guanidine · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I, J
- ADP · Adenosine-5'-diphosphate · ligand · 7 copies · chains A, D, E, I, J, K, L
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 5 copies · chains B, C, F, G, H
- NA · Sodium ion · metal · 17 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, D, C, E, F, H, I, G, K, L
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 | 805 | 0.89 | 0.93 | 68 | empty |
| 2 | 1037 | 0.89 | 0.91 | 99 | empty |
| 3 | 447 | 0.86 | 0.93 | 40 | empty |
| 4 | 411 | 0.84 | 0.92 | 36 | empty |
| 5 | 361 | 0.84 | 0.93 | 34 | empty |
Interfaces
22 interfaces between chains.
- K–L · 2851 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 2830 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2813 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2805 Ų buried · 36 hydrogen bonds · protein-protein
- I–J · 2795 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- P05091 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, mitochondrial (P05091) · a predicted model of the same protein · chain G 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 2ONM · PDBe 2ONM · UniProt P05091
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