MolNFT v1 · #163864 · protein
Crystal structure of DHQ1 from salmonella typhi covalently modified by compound 9
6SFG · 3-dehydroquinate dehydratase: “Crystal structure of DHQ1 from salmonella typhi covalently modified by compound 9”. X-ray diffraction, 2 ligands (FQZ, FSQ), 3 pockets (best druggability 0.69). MolNFT v1 #163864 on GenesisL1: 3D…
- PDB
- 6SFG
- Type
- protein
- Length
- 252 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P24670
- Ligands
- FQZ, FSQ
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 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
- FQZ · (1~{R},3~{S},4~{R},5~{R})-3-methyl-4,5-bis(hydroxyl) cyclohexane-1-carboxylic acid · ligand · chains A
- FSQ · (1~{S},3~{R},4~{S},5~{R})-3-methyl-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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.69 | 0.96 | 20 | FQZ, FSQ |
| 2 | 82 | 0.42 | 0.80 | 21 | empty |
| 3 | 54 | 0.35 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6SFG · Crystal structure of DHQ1 from salmonella typhi covalently modified by compound 9 · 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 6SFG · PDBe 6SFG · UniProt P24670
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