Research workbench
Crystal structure of native daua
Analyse Crystal structure of native daua in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PNU
- Type
- protein
- Length
- 1,922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase | protein | 475 | 42% helix, 24% strand | — |
| B | Aldehyde dehydrogenase | protein | 482 | 41% helix, 21% strand | — |
| C | Aldehyde dehydrogenase | protein | 483 | 41% helix, 22% strand | — |
| D | Aldehyde dehydrogenase | protein | 482 | 41% helix, 22% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.83 | 0.85 | 101 | empty |
| 2 | 723 | 0.81 | 0.84 | 73 | EDO |
| 3 | 74 | 0.75 | 0.98 | 17 | EDO |
| 4 | 80 | 0.74 | 0.97 | 23 | EDO |
| 5 | 82 | 0.74 | 0.97 | 24 | EDO |
Interfaces
4 interfaces between chains.
- A–C · 2653 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 443 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 411 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 346 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6PNU · Crystal structure of native DauA · 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
- Elsewhere: RCSB PDB 6PNU · PDBe 6PNU
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