MolNFT v1 · #16478 · protein
Human mitochondrial aldehyde dehydrogenase complexed with NADH in the presence of MG2+
1O02: “Human mitochondrial aldehyde dehydrogenase complexed with NADH in the presence of MG2+”. X-ray diffraction, 4 ligands (GAI, NAI, MG), 20 pockets (best druggability 0.90). MolNFT v1 #16478 on GenesisL1: 3D structure, binding sites…
- PDB
- 1O02
- Type
- protein
- Length
- 3,952 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- EC
- 1.2.1.3
- UniProt
- P05091
- Ligands
- GAI, NAI, MG, NA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 494 | 40% helix, 21% strand | P05091 |
Ligands and binding sites
- GAI · Guanidine · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 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 · 8 copies · chains A, B, D, C, 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 | 903 | 0.90 | 0.93 | 70 | empty |
| 2 | 928 | 0.90 | 0.92 | 71 | empty |
| 3 | 437 | 0.86 | 0.93 | 42 | empty |
| 4 | 424 | 0.85 | 0.93 | 40 | empty |
| 5 | 181 | 0.83 | 0.98 | 41 | EDO |
Interfaces
13 interfaces between chains.
- G–H · 2872 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 2858 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2854 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2826 Ų buried · 48 hydrogen bonds · protein-protein
- F–G · 1608 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1O02 · Human mitochondrial aldehyde dehydrogenase complexed with NADH in the presence of Mg2+ · 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 B 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 1O02 · PDBe 1O02 · UniProt P05091
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