Research workbench
Crystal structure of the Y248A mutant of C(30) carotenoid dehydrosqualene synthase from staphylococcus aureus in complex with zaragozic acid a
Analyse Crystal structure of the Y248A mutant of C(30) carotenoid dehydrosqualene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VJE
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehydrosqualene synthase
- EC
- 2.5.1.-
- UniProt
- A9JQL9
- Ligands
- ZGA
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehydrosqualene synthase (EC 2.5.1.-) | protein | 284 | 73% helix, 0% strand | A9JQL9 |
Ligands and binding sites
- ZGA · Zaragozic acid A · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.85 | 0.89 | 61 | ZGA |
| 2 | 698 | 0.85 | 0.89 | 71 | ZGA |
| 3 | 136 | 0.73 | 0.92 | 21 | empty |
| 4 | 81 | 0.54 | 0.86 | 21 | empty |
| 5 | 71 | 0.37 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3VJE · Crystal structure of the Y248A mutant of C(30) carotenoid dehydrosqualene synthase from… · the same entry in another collection · chain A against A, TM-score 1.00
- A9JQL9 · AlphaFold monomer V2.0 prediction for 4,4'-diapophytoene synthase (A9JQL9) · 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 A9JQL9
- Elsewhere: RCSB PDB 3VJE · PDBe 3VJE · UniProt A9JQL9
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