Research workbench
Structure of helicobacter pylori type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3-dehydroquinic acid
Analyse Structure of helicobacter pylori type II dehydroquinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XB9
- Type
- protein
- Length
- 474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- Q48255
- Ligands
- XNW
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 158 | 47% helix, 18% strand | Q48255 |
Ligands and binding sites
- XNW · (1R,2R,4S,5R)-1,4,5-trihydroxy-2-(4-methoxybenzyl)-3-oxocyclohexanecarboxylic acid · ligand · 2 copies · chains A, C, B
- CIT · Citric acid · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.75 | 0.93 | 22 | XNW |
| 2 | 163 | 0.73 | 0.91 | 24 | XNW |
| 3 | 50 | 0.70 | 0.98 | 16 | CIT |
| 4 | 214 | 0.56 | 0.79 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–C · 713 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 704 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 687 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2XB9 · Structure of Helicobacter pylori type II dehydroquinase in complex with inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q48255 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (Q48255) · a predicted model of the same protein · chain C 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 Q48255
- Elsewhere: RCSB PDB 2XB9 · PDBe 2XB9 · UniProt Q48255
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