MolNFT v1 · #70230 · protein
Crystal structure of the human squalene synthase complexed with bph- 652
3LEE · Squalene synthetase: “Crystal structure of the human squalene synthase complexed with bph- 652”. X-ray diffraction, 2 ligands (B65, MG), 14 pockets (best druggability 0.79). MolNFT v1 #70230 on GenesisL1: 3D structure, binding sites…
- PDB
- 3LEE
- Type
- protein
- Length
- 1,879 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Squalene synthetase
- EC
- 2.5.1.21
- UniProt
- P37268
- Ligands
- B65, MG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Squalene synthetase (EC 2.5.1.21) | protein | 324 | 70% helix, 0% strand | P37268 |
| D | Squalene synthetase (EC 2.5.1.21) | protein | 322 | 69% helix, 0% strand | P37268 |
| E | Squalene synthetase (EC 2.5.1.21) | protein | 323 | 68% helix, 0% strand | P37268 |
| F | Squalene synthetase (EC 2.5.1.21) | protein | 262 | 71% helix, 0% strand | P37268 |
Ligands and binding sites
- B65 · (1R)-4-(3-phenoxyphenyl)-1-phosphonobutane-1-sulfonic acid · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.79 | 0.82 | 76 | B65, MG |
| 2 | 875 | 0.79 | 0.81 | 72 | B65, MG |
| 3 | 816 | 0.79 | 0.82 | 63 | B65, MG |
| 4 | 898 | 0.79 | 0.81 | 102 | empty |
| 5 | 819 | 0.78 | 0.81 | 79 | B65, MG |
Interfaces
11 interfaces between chains.
- D–F · 718 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 710 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 706 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 699 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 691 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3LEE · Crystal structure of the human squalene synthase complexed with BPH-652 · 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 C 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 3LEE · PDBe 3LEE · UniProt P37268
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