Research workbench
Crystal structure of the human squalene synthase in complex with farnesyl thiopyrophosphate
Analyse Crystal structure of the human squalene synthase in complex with farnesyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WEF
- Type
- protein
- Length
- 1,973 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Squalene synthase
- EC
- 2.5.1.21
- UniProt
- P37268
- Ligands
- FPS
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Squalene synthase (EC 2.5.1.21) | protein | 327 | 72% helix, 0% strand | P37268 |
| B | Squalene synthase (EC 2.5.1.21) | protein | 333 | 71% helix, 0% strand | P37268 |
| C | Squalene synthase (EC 2.5.1.21) | protein | 333 | 71% helix, 0% strand | P37268 |
| D | Squalene synthase (EC 2.5.1.21) | protein | 329 | 71% helix, 0% strand | P37268 |
| E | Squalene synthase (EC 2.5.1.21) | protein | 329 | 71% helix, 0% strand | P37268 |
| F | Squalene synthase (EC 2.5.1.21) | protein | 322 | 70% helix, 0% strand | P37268 |
Ligands and binding sites
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · 8 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.80 | 0.83 | 71 | FPS |
| 2 | 947 | 0.80 | 0.81 | 87 | FPS |
| 3 | 868 | 0.79 | 0.82 | 85 | empty |
| 4 | 714 | 0.79 | 0.83 | 56 | empty |
| 5 | 1038 | 0.79 | 0.80 | 83 | FPS |
Interfaces
11 interfaces between chains.
- A–B · 1015 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 967 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 947 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 906 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 870 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3WEF · Crystal structure of the human squalene synthase in complex with farnesyl… · the same entry in another collection · chain F against F, TM-score 1.00
- P37268 · AlphaFold monomer V2.0 prediction for squalene synthase (P37268) · a predicted model of the same protein · chain F 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 P37268
- Elsewhere: RCSB PDB 3WEF · PDBe 3WEF · UniProt P37268
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