Research workbench
Crystal structure of Putative aldehyde dehydrogenase from Sinorhizobium meliloti 1021
Analyse Crystal structure of Putative aldehyde dehydrogenase from Sinorhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DAL
- Type
- protein
- Length
- 3,806 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Sinorhizobium meliloti
- Molecule
- Putative aldehyde dehydrogenase
- EC
- 1.2.1.-
- UniProt
- Q92ND9
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.3 · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aldehyde dehydrogenase (EC 1.2.1.-) | protein | 475 | 42% helix, 23% strand | Q92ND9 |
| B, C, D, E, F, H | Putative aldehyde dehydrogenase (EC 1.2.1.-) | protein | 476 | 40% helix, 22% strand | Q92ND9 |
| G | Putative aldehyde dehydrogenase (EC 1.2.1.-) | protein | 475 | 41% helix, 22% strand | Q92ND9 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.86 | 0.95 | 33 | empty |
| 2 | 404 | 0.86 | 0.94 | 36 | empty |
| 3 | 398 | 0.86 | 0.94 | 33 | empty |
| 4 | 789 | 0.85 | 0.88 | 83 | empty |
| 5 | 635 | 0.80 | 0.85 | 71 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2661 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2651 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2617 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2566 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1123 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 95 modified (engineered).
Compared structures
- 4DAL · Crystal structure of putative aldehyde 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 Q92ND9
- Elsewhere: RCSB PDB 4DAL · PDBe 4DAL · UniProt Q92ND9
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