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Structure of the salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid derivative
Analyse Structure of the salmonella typhi type I dehydroquinase inhibited by a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CNP
- 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
- 9C4, NA, CL
- Pockets
- 7 · best druggability 0.67
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
- 9C4 · (2S)-2-hydroxy-3-epiquinic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 7 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 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 | 0.67 | 0.95 | 18 | 9C4 |
| 2 | 53 | 0.67 | 0.96 | 18 | 9C4 |
| 3 | 95 | 0.47 | 0.81 | 23 | empty |
| 4 | 85 | 0.44 | 0.80 | 22 | empty |
| 5 | 50 | 0.39 | 0.81 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1093 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4CNP · Structure of the Salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid… · 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 4CNP · PDBe 4CNP · UniProt P24670
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