MolNFT v1 · #90129 · protein
Crystal structure of dehydrosqualene synthase (crtm) from S. aureus complexed with diphosphate and quinuclidine bph-651
4EA0: “Crystal structure of dehydrosqualene synthase (crtm) from S. aureus complexed with diphosphate and…”. X-ray diffraction, 3 ligands (POP, 651, MG), 5 pockets (best druggability 0.90). MolNFT v1 #90129 on GenesisL1: 3D structure…
- PDB
- 4EA0
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehydrosqualene synthase
- EC
- 2.5.1.96
- UniProt
- A9JQL9
- Ligands
- POP, 651, MG
- Pockets
- 5 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehydrosqualene synthase (EC 2.5.1.96) | protein | 284 | 74% helix, 0% strand | A9JQL9 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- 651 · (3R)-3-biphenyl-4-yl-1-azabicyclo[2.2.2]octan-3-ol · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.90 | 0.92 | 126 | MG, POP, TLA, 651 |
| 2 | 303 | 0.56 | 0.76 | 41 | empty |
| 3 | 119 | 0.48 | 0.79 | 20 | empty |
| 4 | 51 | 0.33 | 0.77 | 10 | empty |
| 5 | 53 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 943 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4EA0 · Crystal structure of dehydrosqualene synthase (Crtm) from S. aureus complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- A9JQL9 · AlphaFold monomer V2.0 prediction for 4,4'-diapophytoene synthase (A9JQL9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 4EA0 · PDBe 4EA0 · UniProt A9JQL9
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