Research workbench
2.4A Crystal structure of Staphylococcus aureus type I 3-dehydroquinase, with 3-dehydroquinate bound
Analyse 2.4A Crystal structure of Staphylococcus aureus type I 3-dehydroquinase, with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SFJ
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Staphylococcus aureus subsp. aureus
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- Q6GII7
- Ligands
- DHK
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 227 | 41% helix, 22% strand | Q6GII7 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 233 | 41% helix, 21% strand | Q6GII7 |
Ligands and binding sites
- DHK · 3-dehydroshikimate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.61 | 0.90 | 21 | DHK |
| 2 | 70 | 0.60 | 0.90 | 23 | DHK |
| 3 | 64 | 0.39 | 0.79 | 13 | empty |
| 4 | 50 | 0.31 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1061 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1SFJ · 2.4A crystal structure of staphylococcus aureus type I 3- dehydroquinase, with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GII7 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (Q6GII7) · a predicted model of the same protein · chain A 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 Q6GII7
- Elsewhere: RCSB PDB 1SFJ · PDBe 1SFJ · UniProt Q6GII7
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