Research workbench
Structure and function of aldehyde dehydrogenase from thermus thermophilus: an enzyme with an evolutionarily-distinct C-terminal arm (recombinant protein with shortened C-terminal, ADH508)
Analyse Structure and function of aldehyde dehydrogenase from thermus thermophilus: an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FKV
- Type
- protein
- Length
- 1,009 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- EC
- 1.2.1.3
- UniProt
- Q72KD3
- Ligands
- SO4, CL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 504 | 39% helix, 23% strand | Q72KD3 |
| B | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 505 | 39% helix, 23% strand | Q72KD3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.78 | 0.84 | 78 | PEG, SO4, CL |
| 2 | 730 | 0.74 | 0.80 | 92 | PEG |
| 3 | 433 | 0.70 | 0.81 | 50 | empty |
| 4 | 313 | 0.69 | 0.83 | 47 | TRS, SO4 |
| 5 | 229 | 0.56 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3241 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 6FKV · Structure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme… · 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 Q72KD3
- Elsewhere: RCSB PDB 6FKV · PDBe 6FKV · UniProt Q72KD3
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