Research workbench
Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 4
Analyse Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H5J
- Type
- protein
- Length
- 252 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Salmonella typhi
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P24670
- Ligands
- FT5
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.4 · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 252 | 46% helix, 21% strand | P24670 |
Ligands and binding sites
- FT5 · (3~{R})-3,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.65 | 0.95 | 19 | FT5 |
| 2 | 90 | 0.44 | 0.80 | 21 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6H5J · Crystal structure of DHQ1 from salmonella typhi covalently modified by ligand 4 · the same entry in another collection · chain A against A, TM-score 1.00
- P24670 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P24670) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P24670
- Elsewhere: RCSB PDB 6H5J · PDBe 6H5J · UniProt P24670
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