Research workbench
Structure of ALDH7A1 mutant E399D complexed with NAD
Analyse Structure of ALDH7A1 mutant E399D complexed with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O4L
- Type
- protein
- Length
- 2,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens
- Molecule
- Alpha-aminoadipic semialdehyde dehydrogenase
- EC
- 1.2.1.31, 1.2.1.3, 1.2.1.8
- UniProt
- P49419
- Ligands
- NAD, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 1.85 · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-aminoadipic semialdehyde dehydrogenase (EC 1.2.1.31, 1.2.1.3, 1.2.1.8) | protein | 508 | 41% helix, 22% strand | P49419 |
| B | Alpha-aminoadipic semialdehyde dehydrogenase (EC 1.2.1.31, 1.2.1.3, 1.2.1.8) | protein | 507 | 41% helix, 22% strand | P49419 |
| D | Alpha-aminoadipic semialdehyde dehydrogenase (EC 1.2.1.31, 1.2.1.3, 1.2.1.8) | protein | 509 | 41% helix, 22% strand | P49419 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.87 | 0.88 | 87 | empty |
| 2 | 1103 | 0.86 | 0.88 | 84 | empty |
| 3 | 1134 | 0.86 | 0.87 | 64 | empty |
| 4 | 342 | 0.80 | 0.90 | 45 | empty |
| 5 | 314 | 0.79 | 0.90 | 40 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3892 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 3759 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 974 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 973 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 930 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6O4L · Structure of ALDH7A1 mutant E399D complexed with NAD · the same entry in another collection · chain D against D, TM-score 1.00
- P49419 · AlphaFold monomer V2.0 prediction for alpha-aminoadipic semialdehyde dehydrogenase… · a predicted model of the same protein · chain A 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 P49419
- Elsewhere: RCSB PDB 6O4L · PDBe 6O4L · UniProt P49419
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