Research workbench
Crystals structure of aspartate beta-semialdehyde dehydrogenase from vibrio cholerae with product of S-allyl-L-cysteine sulfoxide
Analyse Crystals structure of aspartate beta-semialdehyde dehydrogenase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q0E
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate-semialdehyde dehydrogenase
- EC
- 1.2.1.11
- UniProt
- Q9KQG2
- Ligands
- CYS, SO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 369 | 40% helix, 23% strand | Q9KQG2 |
Ligands and binding sites
- CYS · Cysteine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.63 | 0.77 | 53 | SO4, CYS, EDO |
| 2 | 349 | 0.61 | 0.78 | 44 | CYS |
| 3 | 70 | 0.34 | 0.76 | 15 | EDO |
| 4 | 71 | 0.33 | 0.75 | 15 | empty |
| 5 | 54 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3517 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3Q0E · Crystals Structure of Aspartate beta-Semialdehyde Dehydrogenase from Vibrio Cholerae with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQG2 · AlphaFold monomer V2.0 prediction for aspartate-semialdehyde dehydrogenase 1 (Q9KQG2) · 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 Q9KQG2
- Elsewhere: RCSB PDB 3Q0E · PDBe 3Q0E · UniProt Q9KQG2
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