MolNFT v1 · #89717 · protein
Crystal structure of trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(N-PROPYLAMINO)ETHANE-1,1-DIYL]BISPHOSPHONIC acid and MG2+
4DXJ · Farnesyl pyrophosphate synthase: “Crystal structure of trypanosome cruzi farnesyl diphosphate synthase in complex with…”. X-ray diffraction, 4 ligands (0M9, IPE, MG), 12 pockets (best druggability 0.82). MolNFT v1 #89717 on…
- PDB
- 4DXJ
- Type
- protein
- Length
- 1,086 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.10
- UniProt
- Q95WL3
- Ligands
- 0M9, IPE, MG, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 362 | 73% helix, 1% strand | Q95WL3 |
Ligands and binding sites
- 0M9 · [2-(propylamino)ethane-1,1-diyl]bis(phosphonic acid) · ligand · 3 copies · chains A, B, C
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 9 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains A, B
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.82 | 0.93 | 45 | MG, 0M9, IPE |
| 2 | 287 | 0.81 | 0.92 | 45 | MG, 0M9, IPE |
| 3 | 263 | 0.80 | 0.92 | 44 | MG, 0M9, IPE |
| 4 | 102 | 0.79 | 0.98 | 20 | PGE |
| 5 | 208 | 0.49 | 0.76 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3141 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 308 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4DXJ · Crystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with… · the same entry in another collection · 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 Q95WL3
- Elsewhere: RCSB PDB 4DXJ · PDBe 4DXJ · UniProt Q95WL3
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