Research workbench
Crystal structure of a semialdehyde dehydrogenase from sinorhizobium meliloti 1021
Analyse Crystal structure of a semialdehyde dehydrogenase from sinorhizobium meliloti… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V4C
- Type
- protein
- Length
- 1,004 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase (NADP+)
- EC
- 1.2.1.4
- UniProt
- Q92WS7
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (NADP+) (EC 1.2.1.4) | protein | 504 | 45% helix, 19% strand | Q92WS7 |
| B | Aldehyde dehydrogenase (NADP+) (EC 1.2.1.4) | protein | 500 | 45% helix, 18% strand | Q92WS7 |
Ligands and binding sites
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.87 | 0.91 | 70 | empty |
| 2 | 211 | 0.67 | 0.85 | 36 | empty |
| 3 | 446 | 0.63 | 0.76 | 58 | empty |
| 4 | 442 | 0.61 | 0.76 | 54 | empty |
| 5 | 274 | 0.55 | 0.76 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 3269 Ų buried · 73 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3V4C · Crystal structure of a semialdehyde dehydrogenase from Sinorhizobium meliloti 1021 · the same entry in another collection · 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 Q92WS7
- Elsewhere: RCSB PDB 3V4C · PDBe 3V4C · UniProt Q92WS7
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