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, in complex with NADP)
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
- 6FKU
- Type
- protein
- Length
- 1,018 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
- NAP, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 511 | 40% helix, 22% strand | Q72KD3 |
| B | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 507 | 40% helix, 21% strand | Q72KD3 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.78 | 0.83 | 93 | NAP, SO4 |
| 2 | 1024 | 0.77 | 0.79 | 120 | PG4, PGE, 1PE |
| 3 | 561 | 0.75 | 0.82 | 82 | NAP, SO4 |
| 4 | 245 | 0.57 | 0.78 | 22 | 1PE |
| 5 | 128 | 0.44 | 0.76 | 18 | PGE |
Interfaces
1 interface between chains.
- A–B · 3496 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 6FKU · 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 6FKU · PDBe 6FKU · UniProt Q72KD3
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