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Crystal structure of an acetylating aldehyde dehydrogenase from geobacillus thermoglucosidasius
Analyse Crystal structure of an acetylating aldehyde dehydrogenase from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J78
- Type
- protein
- Length
- 1,811 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetaldehyde dehydrogenase (acetylating)
- EC
- 1.2.1.10
- UniProt
- A0A0M1QQ83
- Ligands
- MG
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) | protein | 453 | 46% helix, 19% strand | A0A0M1QQ83 |
| D | Acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) | protein | 452 | 46% helix, 19% strand | A0A0M1QQ83 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 35 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.68 | 0.78 | 71 | GOL |
| 2 | 620 | 0.68 | 0.77 | 65 | GOL |
| 3 | 359 | 0.63 | 0.78 | 53 | ACT |
| 4 | 325 | 0.63 | 0.79 | 49 | ACT, GOL |
| 5 | 454 | 0.63 | 0.77 | 54 | MG, GOL |
Interfaces
6 interfaces between chains.
- A–B · 3235 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 3138 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 479 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 43 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5J78 · Crystal structure of an Acetylating Aldehyde Dehydrogenase from Geobacillus… · 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 A0A0M1QQ83
- Elsewhere: RCSB PDB 5J78 · PDBe 5J78 · UniProt A0A0M1QQ83
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