Research workbench
Crystal structure of a geobacillus thermoglucosidasius acetylating aldehyde dehydrogenase in complex with ADP
Analyse Crystal structure of a geobacillus thermoglucosidasius acetylating aldehyde… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J7I
- Type
- protein
- Length
- 1,819 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
- ADP, APR
- Pockets
- 18 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) | protein | 455 | 45% helix, 19% strand | A0A0M1QQ83 |
| B | Acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) | protein | 456 | 46% helix, 19% strand | A0A0M1QQ83 |
| C | Acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) | protein | 455 | 46% helix, 20% strand | A0A0M1QQ83 |
| D | Acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) | protein | 453 | 46% helix, 19% strand | A0A0M1QQ83 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, C, D
- APR · Adenosine-5-diphosphoribose · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.67 | 0.77 | 67 | empty |
| 2 | 534 | 0.67 | 0.78 | 43 | empty |
| 3 | 634 | 0.65 | 0.75 | 80 | ADP |
| 4 | 359 | 0.62 | 0.78 | 52 | empty |
| 5 | 361 | 0.61 | 0.77 | 55 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3236 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 2961 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 556 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 5J7I · Crystal structure of a Geobacillus thermoglucosidasius Acetylating Aldehyde Dehydrogenase… · 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 5J7I · PDBe 5J7I · UniProt A0A0M1QQ83
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.