Research workbench
Structure of helicobacter pylori type II dehydroquinase with a new carbasugar-thiophene inhibitor.
Analyse Structure of helicobacter pylori type II dehydroquinase with a new… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WKS
- Type
- protein
- Length
- 918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- Q48255
- Ligands
- CB6
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 153 | 48% helix, 18% strand | Q48255 |
Ligands and binding sites
- CB6 · (1R,4S,5R)-1,4,5-trihydroxy-3-[(5-methyl-1-benzothiophen-2-yl)methoxy]cyclohex-2-ene-1-carboxylic acid · ligand · 6 copies · chains A, B, E, C, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.74 | 0.93 | 23 | CB6 |
| 2 | 127 | 0.74 | 0.93 | 26 | CB6 |
| 3 | 137 | 0.73 | 0.92 | 22 | CB6 |
| 4 | 127 | 0.73 | 0.93 | 25 | CB6 |
| 5 | 137 | 0.73 | 0.92 | 26 | CB6 |
Interfaces
7 interfaces between chains.
- B–C · 972 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 686 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 681 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 675 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 675 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2WKS · Structure of Helicobacter pylori Type II Dehydroquinase with a new carbasugar-thiophene… · the same entry in another collection · chain F against F, TM-score 1.00
- Q48255 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (Q48255) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 2WKS · PDBe 2WKS · UniProt Q48255
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