Research workbench
Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Non-Covalent Complex with Dehydroquinate.
Analyse Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehydratase (aroD)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NNT
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Salmonella enterica subsp. enterica serovar Typhimurium
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P58687
- Ligands
- DQA
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 257 | 44% helix, 21% strand | P58687 |
Ligands and binding sites
- DQA · 1,3,4-trihydroxy-5-oxo-cyclohexanecarboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.68 | 0.93 | 20 | DQA |
| 2 | 61 | 0.65 | 0.94 | 20 | DQA |
| 3 | 93 | 0.45 | 0.80 | 21 | empty |
| 4 | 74 | 0.43 | 0.80 | 21 | empty |
| 5 | 86 | 0.42 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3NNT · Crystal structure of K170M mutant of type I 3-dehydroquinate dehydratase (arod) from… · the same entry in another collection · chain A against A, TM-score 1.00
- P58687 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P58687) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P58687
- Elsewhere: RCSB PDB 3NNT · PDBe 3NNT · UniProt P58687
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