Research workbench
X-ray crystal structure of fatty aldehyde dehydrogenase enzymes from marinobacter aquaeolei VT8 complexed with a substrate
Analyse X-ray crystal structure of fatty aldehyde dehydrogenase enzymes from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U0L
- Type
- protein
- Length
- 975 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-succinylglutamate 5-semialdehyde dehydrogenase
- EC
- 1.2.1.71
- UniProt
- A1U5W8
- Ligands
- 8YP, CL, PO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-succinylglutamate 5-semialdehyde dehydrogenase (EC 1.2.1.71) | protein | 488 | 39% helix, 22% strand | A1U5W8 |
| B | N-succinylglutamate 5-semialdehyde dehydrogenase (EC 1.2.1.71) | protein | 487 | 38% helix, 22% strand | A1U5W8 |
Ligands and binding sites
- 8YP · decanal · ligand · chains A
- CL · Chloride ion · ion · chains B
- PO4 · Phosphate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.81 | 0.98 | 45 | EDO |
| 2 | 849 | 0.76 | 0.80 | 89 | EDO, 8YP |
| 3 | 66 | 0.73 | 0.98 | 22 | MPD |
| 4 | 480 | 0.69 | 0.80 | 51 | empty |
| 5 | 544 | 0.68 | 0.78 | 67 | empty |
Interfaces
1 interface between chains.
- A–B · 4055 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 5U0L · X-ray crystal structure of fatty aldehyde dehydrogenase enzymes from Marinobacter… · the same entry in another collection · chain A against A, TM-score 1.00
- A1U5W8 · AlphaFold monomer V2.0 prediction for N-succinylglutamate 5-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 A1U5W8
- Elsewhere: RCSB PDB 5U0L · PDBe 5U0L · UniProt A1U5W8
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