Research workbench
Crystal structure of a squalene cyclase in complex with the potential anticholesteremic drug RO48-8071
Analyse Crystal structure of a squalene cyclase in complex with the potential… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GSZ
- Type
- protein
- Length
- 1,857 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Squalene--hopene cyclase
- EC
- 5.4.99.17
- UniProt
- P33247
- Ligands
- R71
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Squalene--hopene cyclase (EC 5.4.99.17) | protein | 619 | 52% helix, 4% strand | P33247 |
Ligands and binding sites
- R71 · [4-({6-[allyl(methyl)amino]hexyl}oxy)-2-fluorophenyl](4-bromophenyl)methanone · ligand · 3 copies · chains A, B, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.86 | 0.95 | 59 | R71 |
| 2 | 506 | 0.84 | 0.90 | 75 | R71 |
| 3 | 506 | 0.84 | 0.90 | 70 | R71 |
| 4 | 90 | 0.75 | 0.97 | 20 | empty |
| 5 | 217 | 0.66 | 0.84 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–C · 568 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 556 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1GSZ · Crystal Structure of a Squalene Cyclase in Complex with the Potential Anticholesteremic… · the same entry in another collection · chain A against A, TM-score 1.00
- P33247 · AlphaFold monomer V2.0 prediction for squalene--hopene cyclase (P33247) · 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 P33247
- Elsewhere: RCSB PDB 1GSZ · PDBe 1GSZ · UniProt P33247
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