MolNFT v1 · #13388 · protein
Crystal structure of 3-dehydroquinase from salmonella typhi complexed with reaction product
1L9W · 3-dehydroquinate dehydratase arod: “Crystal structure of 3-dehydroquinase from salmonella typhi complexed with reaction product”. X-ray diffraction, 1 ligand (DHS), 9 pockets (best druggability 0.71). MolNFT v1 #13388 on GenesisL1…
- PDB
- 1L9W
- Type
- protein
- Length
- 1,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase arod
- EC
- 4.2.1.10
- UniProt
- P24670
- Ligands
- DHS
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-dehydroquinate dehydratase arod (EC 4.2.1.10) | protein | 252 | 46% helix, 20% strand | P24670 |
Ligands and binding sites
- DHS · 3-amino-4,5-dihydroxy-cyclohex-1-enecarboxylate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.71 | 0.97 | 19 | DHS |
| 2 | 62 | 0.70 | 0.97 | 17 | DHS |
| 3 | 60 | 0.69 | 0.96 | 17 | DHS |
| 4 | 62 | 0.66 | 0.94 | 19 | DHS |
| 5 | 414 | 0.60 | 0.76 | 40 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1139 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1133 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 341 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1L9W · Crystal structure of 3-dehydroquinase from salmonella typhi complexed with reaction… · the same entry in another collection · chain C against C, TM-score 1.00
- P24670 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P24670) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 1L9W · PDBe 1L9W · UniProt P24670
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