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Crystal structure of mycobacterium tuberculosis type II dehydroquinase D88N mutant inhibited by a 3-dehydroquinic acid derivative
Analyse Crystal structure of mycobacterium tuberculosis type II dehydroquinase D88N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V0S
- Type
- protein
- Length
- 283 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
- P9WPX6
- Ligands
- 2HN, 7HN, NA, CL
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 140 | 44% helix, 19% strand | P9WPX6 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 143 | 43% helix, 17% strand | P9WPX6 |
Ligands and binding sites
- 2HN · (1R,2S,4S,5R)-2-(2,3,4,5,6-pentafluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid · ligand · 3 copies · chains A, B
- 7HN · 3,4-dihydroxy-2-[(2,3,4,5,6-pentafluorophenyl)methyl]benzoic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.59 | 0.83 | 22 | 2HN |
| 2 | 132 | 0.55 | 0.82 | 17 | 2HN |
| 3 | 100 | 0.40 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4V0S · Crystal structure of Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPX6 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P9WPX6) · a predicted model of the same protein · chain A 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 P9WPX6
- Elsewhere: RCSB PDB 4V0S · PDBe 4V0S · UniProt P9WPX6
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