Research workbench
Crystal structure of DHQ1 from salmonella typhi covalently modified by ligand 2
Analyse Crystal structure of DHQ1 from salmonella typhi covalently modified by ligand 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H5D
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P24670
- Ligands
- WPL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 252 | 46% helix, 20% strand | P24670 |
Ligands and binding sites
- WPL · (1~{S},3~{S},4~{R},5~{R})-3-methyl-1,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.70 | 0.97 | 19 | WPL |
| 2 | 59 | 0.65 | 0.94 | 21 | WPL |
| 3 | 88 | 0.43 | 0.79 | 19 | empty |
| 4 | 73 | 0.38 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1101 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6H5D · Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 2 · 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 B 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 6H5D · PDBe 6H5D · UniProt P24670
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