Research workbench
Crystal structure of DHQ1 from staphylococcus aureus covalently modified by ligand 7
Analyse Crystal structure of DHQ1 from staphylococcus aureus covalently modified by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SFH
- Type
- protein
- Length
- 474 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
- Q2YWJ9
- Ligands
- L9Z, LI, SO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 237 | 43% helix, 21% strand | Q2YWJ9 |
Ligands and binding sites
- L9Z · (1~{S},3~{S},4~{S},5~{R})-3-(aminomethyl)-3,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid · ligand · 2 copies · chains A, B
- LI · Lithium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.68 | 0.92 | 22 | L9Z |
| 2 | 85 | 0.66 | 0.92 | 24 | L9Z |
Interfaces
1 interface between chains.
- A–B · 920 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6SFH · CRYSTAL STRUCTURE OF DHQ1 FROM Staphylococcus aureus COVALENTLY MODIFIED BY LIGAND 7 · the same entry in another collection · chain A against A, TM-score 1.00
- Q2YWJ9 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (Q2YWJ9) · a predicted model of the same protein · chain B 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 Q2YWJ9
- Elsewhere: RCSB PDB 6SFH · PDBe 6SFH · UniProt Q2YWJ9
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