MolNFT v1 · #30139 · protein
Human mitochondrial aldehyde dehydrogenase asian variant, ALDH2*2, apo form
1ZUM: “Human mitochondrial aldehyde dehydrogenase asian variant, ALDH2*2, apo form”. X-ray diffraction, 2 ligands (GAI, NA), 20 pockets (best druggability 0.89). MolNFT v1 #30139 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1ZUM
- Type
- protein
- Length
- 5,598 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- EC
- 1.2.1.3
- UniProt
- P05091
- Ligands
- GAI, NA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 9 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 469 | 41% helix, 22% strand | P05091 |
| B | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 465 | 39% helix, 21% strand | P05091 |
| C, F | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 468 | 39% helix, 22% strand | P05091 |
| D | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 468 | 39% helix, 22% strand | P05091 |
| E, G, H | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 469 | 39% helix, 23% strand | P05091 |
| I | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 468 | 39% helix, 22% strand | P05091 |
| J | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 467 | 39% helix, 22% strand | P05091 |
| K | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 456 | 40% helix, 21% strand | P05091 |
| L | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 462 | 39% helix, 21% strand | P05091 |
Ligands and binding sites
- GAI · Guanidine · ligand · 8 copies · chains A, B, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B, D, C, H, E, F, G, I, J, 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 | 1001 | 0.89 | 0.90 | 111 | empty |
| 2 | 946 | 0.87 | 0.88 | 90 | empty |
| 3 | 523 | 0.86 | 0.92 | 42 | empty |
| 4 | 200 | 0.83 | 0.97 | 40 | empty |
| 5 | 194 | 0.83 | 0.97 | 38 | EDO |
Interfaces
22 interfaces between chains.
- G–H · 2068 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 2014 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2003 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1969 Ų buried · 29 hydrogen bonds · protein-protein
- K–L · 1837 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1ZUM · Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form · the same entry in another collection · chain L against L, 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 1ZUM · PDBe 1ZUM · UniProt P05091
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