Research workbench
Human mitochondrial aldehyde dehydrogenase complexed with agonist alda-1
Analyse Human mitochondrial aldehyde dehydrogenase complexed with agonist alda-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3INJ
- Type
- protein
- Length
- 3,953 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
- GAI, BXB, NA
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 494 | 40% helix, 22% strand | P05091 |
| H | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 495 | 41% helix, 22% strand | P05091 |
Ligands and binding sites
- GAI · Guanidine · ligand · 9 copies · chains A, B, C, D, E, F, G, H
- 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 · 16 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 | 1139 | 0.91 | 0.94 | 102 | empty |
| 2 | 914 | 0.90 | 0.93 | 83 | EDO |
| 3 | 412 | 0.85 | 0.93 | 40 | empty |
| 4 | 723 | 0.83 | 0.87 | 116 | EDO, BXB |
| 5 | 182 | 0.82 | 0.97 | 35 | EDO |
Interfaces
14 interfaces between chains.
- E–F · 2872 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2868 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2857 Ų buried · 51 hydrogen bonds · protein-protein
- G–H · 2818 Ų buried · 44 hydrogen bonds · protein-protein
- F–G · 1606 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3INJ · Human Mitochondrial Aldehyde Dehydrogenase complexed with agonist Alda-1 · 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 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 3INJ · PDBe 3INJ · UniProt P05091
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