Research workbench
Metagenome-derived salicylaldehyde dehydrogenase from alpine soil in complex with protocatechuic acid
Analyse Metagenome-derived salicylaldehyde dehydrogenase from alpine soil in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QHN
- Type
- protein
- Length
- 1,864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Salicylaldehyde dehydrogenase
- Ligands
- DHB
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Salicylaldehyde dehydrogenase | protein | 466 | 43% helix, 21% strand | — |
Ligands and binding sites
- DHB · 3,4-dihydroxybenzoic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.85 | 0.86 | 140 | empty |
| 2 | 995 | 0.83 | 0.85 | 108 | GOL |
| 3 | 1108 | 0.78 | 0.80 | 138 | DHB |
| 4 | 949 | 0.78 | 0.80 | 124 | DHB |
| 5 | 1166 | 0.76 | 0.78 | 124 | DHB |
Interfaces
5 interfaces between chains.
- A–C · 3299 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 3292 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 217 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 210 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6QHN · Metagenome-derived salicylaldehyde dehydrogenase from alpine soil in complex with… · 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 6QHN · PDBe 6QHN
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