Research workbench
Structure of the salmonella typhi type I dehydroquinase inhibited by a 3-dehydroquinic 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
- 4CNO
- Type
- protein
- Length
- 989 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P24670
- Ligands
- 9PY
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 247 | 45% helix, 21% strand | P24670 |
| C | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 248 | 45% helix, 20% strand | P24670 |
Ligands and binding sites
- 9PY · (2R)-2-methyl-3-dehydroquinic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.62 | 0.80 | 32 | 9PY |
| 2 | 527 | 0.62 | 0.75 | 42 | empty |
| 3 | 226 | 0.62 | 0.81 | 30 | 9PY |
| 4 | 388 | 0.60 | 0.77 | 53 | empty |
| 5 | 255 | 0.60 | 0.79 | 31 | 9PY |
Interfaces
3 interfaces between chains.
- A–B · 344 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 339 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 111 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CNO · Structure of the Salmonella typhi Type I dehydroquinase inhibited by a 3-dehydroquinic… · the same entry in another collection · chain D against D, TM-score 1.00
- P24670 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P24670) · a predicted model of the same protein · chain D 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 4CNO · PDBe 4CNO · UniProt P24670
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