Research workbench
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from staphylococcus aureus complexed with geranylgeranyl thiopyrophosphate
Analyse Crystal structure of the C(30) carotenoid dehydrosqualene synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AE0
- 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
- GGS, MG
- Pockets
- 8 · 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
- GGS · Phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6, 10,14-tetraenyl]sulfanyl-phosphinic acid · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.85 | 0.93 | 36 | GGS, MG |
| 2 | 330 | 0.84 | 0.93 | 35 | GGS |
| 3 | 160 | 0.74 | 0.92 | 30 | empty |
| 4 | 116 | 0.66 | 0.90 | 24 | empty |
| 5 | 67 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 975 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3AE0 · Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus… · 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 A 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 3AE0 · PDBe 3AE0 · UniProt A9JQL9
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