MolNFT v1 · #82326 · protein
Crystal structure of the human squalene synthase in complex with zaragozic acid a
3VJC: “Crystal structure of the human squalene synthase in complex with zaragozic acid a”. X-ray diffraction, 3 ligands (ZGA, MG, PO4), 16 pockets (best druggability 0.83). MolNFT v1 #82326 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3VJC
- Type
- protein
- Length
- 1,997 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
- ZGA, MG, PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Squalene synthase (EC 2.5.1.21) | protein | 334 | 72% helix, 0% strand | P37268 |
| B, D, E | Squalene synthase (EC 2.5.1.21) | protein | 333 | 71% helix, 0% strand | P37268 |
| C | Squalene synthase (EC 2.5.1.21) | protein | 332 | 72% helix, 0% strand | P37268 |
| F | Squalene synthase (EC 2.5.1.21) | protein | 332 | 70% helix, 0% strand | P37268 |
Ligands and binding sites
- ZGA · Zaragozic acid A · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 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
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.83 | 0.84 | 114 | ZGA |
| 2 | 948 | 0.82 | 0.83 | 103 | ZGA |
| 3 | 787 | 0.81 | 0.84 | 73 | ZGA |
| 4 | 962 | 0.80 | 0.82 | 110 | empty |
| 5 | 802 | 0.80 | 0.83 | 64 | ZGA |
Interfaces
11 interfaces between chains.
- A–B · 1034 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1006 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 987 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 973 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 943 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3VJC · Crystal structure of the human squalene synthase in complex with zaragozic acid A · 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 0.97
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 3VJC · PDBe 3VJC · UniProt P37268
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