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Structure of the human aldehyde dehydrogenase 9A1 in C2 space group
Analyse Structure of the human aldehyde dehydrogenase 9A1 in C2 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QAP
- Type
- protein
- Length
- 1,882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-trimethylaminobutyraldehyde dehydrogenase
- EC
- 1.2.1.47, 1.2.1.3, 1.2.1.19
- UniProt
- P49189
- Ligands
- NA
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-trimethylaminobutyraldehyde dehydrogenase (EC 1.2.1.47, 1.2.1.3, 1.2.1.19) | protein | 470 | 41% helix, 21% strand | P49189 |
| C, D | 4-trimethylaminobutyraldehyde dehydrogenase (EC 1.2.1.47, 1.2.1.3, 1.2.1.19) | protein | 471 | 41% helix, 22% strand | P49189 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains C, D, A
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.89 | 0.91 | 126 | EDO |
| 2 | 751 | 0.81 | 0.85 | 108 | EDO, NA |
| 3 | 708 | 0.81 | 0.85 | 105 | EDO, PEG |
| 4 | 570 | 0.72 | 0.80 | 60 | empty |
| 5 | 536 | 0.68 | 0.78 | 52 | NA, PEG |
Interfaces
6 interfaces between chains.
- C–D · 2868 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2865 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1171 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1131 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 623 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6QAP · Structure of the human aldehyde dehydrogenase 9A1 in C2 space group · the same entry in another collection · chain D against D, TM-score 1.00
- P49189 · AlphaFold monomer V2.0 prediction for 4-trimethylaminobutyraldehyde dehydrogenase (P49189) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P49189
- Elsewhere: RCSB PDB 6QAP · PDBe 6QAP · UniProt P49189
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