MolNFT v1 · #158780 · protein
Structure of ALDH7A1 mutant W175A complexed with L-pipecolic acid
6O4D · Alpha-aminoadipic semialdehyde dehydrogenase: “Structure of ALDH7A1 mutant W175A complexed with L-pipecolic acid”. X-ray diffraction, 1 ligand (6PC), 20 pockets (best druggability 0.87). MolNFT v1 #158780 on GenesisL1: 3D structure…
- PDB
- 6O4D
- Type
- protein
- Length
- 4,070 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-aminoadipic semialdehyde dehydrogenase
- EC
- 1.2.1.31, 1.2.1.3, 1.2.1.8
- UniProt
- P49419
- Ligands
- 6PC
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | 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 | 510 | 41% helix, 22% strand | P49419 |
| D, E, F, H | 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
- 6PC · Pyridine-2-carboxylic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PGE · Triethylene glycol · additive · 6 copies · chains A, D, E, H
- PG4 · Tetraethylene glycol · additive · 5 copies · chains C, D, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, E, F, H
- 1PE · Pentaethylene glycol · additive · chains B
- EDO · 1,2-ethanediol · additive · chains H
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 | 1073 | 0.87 | 0.88 | 87 | PGE, 1PE |
| 2 | 1099 | 0.87 | 0.88 | 87 | PG4 |
| 3 | 1130 | 0.87 | 0.88 | 88 | PG4 |
| 4 | 1014 | 0.87 | 0.88 | 66 | PEG, EDO |
| 5 | 1112 | 0.87 | 0.88 | 84 | PGE, PG4 |
Interfaces
16 interfaces between chains.
- G–H · 3904 Ų buried · 59 hydrogen bonds · protein-protein
- E–F · 3876 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3836 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3772 Ų buried · 57 hydrogen bonds · protein-protein
- B–D · 984 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 6O4D · Structure of ALDH7A1 mutant W175A complexed with L-pipecolic acid · the same entry in another collection · chain H against H, 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 0.99
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 6O4D · PDBe 6O4D · UniProt P49419
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