MolNFT v1 · #70318 · protein
Crystal structure of dehydrosqualene synthase Y129A from S. aureus complexed with presqualene pyrophosphate
3LGZ: “Crystal structure of dehydrosqualene synthase Y129A from S. aureus complexed with presqualene pyrophosphate”. X-ray diffraction, 2 ligands (PS7, MG), 2 pockets (best druggability 0.80). MolNFT v1 #70318 on GenesisL1: 3D structure…
- PDB
- 3LGZ
- Type
- protein
- Length
- 279 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehydrosqualene synthase
- EC
- 2.5.1.-
- UniProt
- A9JQL9
- Ligands
- PS7, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dehydrosqualene synthase (EC 2.5.1.-) | protein | 279 | 74% helix, 0% strand | A9JQL9 |
Ligands and binding sites
- PS7 · {(1R,2R,3R)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-2-methyl-3-[(1E,5E)-2,6,10-trimethylundeca-1,5,9-trien-1-yl]cyclopropyl}methyl trihydrogen diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.80 | 0.83 | 63 | PS7, MG |
| 2 | 53 | 0.33 | 0.77 | 11 | empty |
Compared structures
- 3LGZ · Crystal structure of dehydrosqualene synthase Y129A from S. aureus complexed with… · the same entry in another collection · chain B against B, 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 3LGZ · PDBe 3LGZ · UniProt A9JQL9
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