Research workbench
Crystal structure of putative aldehyde dehydrogenase from sinorhizobium meliloti 1021 complexed with NAD
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
- 4F3X
- Type
- protein
- Length
- 1,903 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aldehyde dehydrogenase
- EC
- 1.2.1.-
- UniProt
- Q92ND9
- Ligands
- NAD
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative aldehyde dehydrogenase (EC 1.2.1.-) | protein | 476 | 40% helix, 23% strand | Q92ND9 |
| D | Putative aldehyde dehydrogenase (EC 1.2.1.-) | protein | 475 | 40% helix, 23% strand | Q92ND9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.86 | 0.94 | 31 | empty |
| 2 | 383 | 0.86 | 0.94 | 31 | empty |
| 3 | 787 | 0.76 | 0.80 | 82 | NAD |
| 4 | 869 | 0.75 | 0.79 | 99 | NAD |
| 5 | 457 | 0.74 | 0.84 | 58 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2670 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2611 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1105 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1105 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1102 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 modified (engineered).
Compared structures
- 4F3X · 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 4F3X · PDBe 4F3X · UniProt Q92ND9
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