MolNFT v1 · #150826 · protein
Crystal structure of DHQ1 from salmonella typhi covalently modified by ligand 1
6H5C · 3-dehydroquinate dehydratase: “Crystal structure of DHQ1 from salmonella typhi covalently modified by ligand 1”. X-ray diffraction, 1 ligand (FSQ), 5 pockets (best druggability 0.68). MolNFT v1 #150826 on GenesisL1: 3D structure…
- PDB
- 6H5C
- 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
- FSQ
- Pockets
- 5 · best druggability 0.68
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
- FSQ · (1~{S},3~{R},4~{S},5~{R})-3-methyl-3,4,5-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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.68 | 0.96 | 19 | FSQ |
| 2 | 54 | 0.67 | 0.96 | 18 | FSQ |
| 3 | 133 | 0.50 | 0.80 | 27 | empty |
| 4 | 85 | 0.44 | 0.80 | 21 | empty |
| 5 | 51 | 0.36 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1125 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6H5C · Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 1 · 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 6H5C · PDBe 6H5C · UniProt P24670
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