MolNFT v1 · #28543 · protein
Structure of the complex of trypanosoma cruzi farnesyl disphosphate synthase with alendronate, isopentenyl diphosphate and MG+2
1YHM · Farnesyl pyrophosphate synthase: “Structure of the complex of trypanosoma cruzi farnesyl disphosphate synthase with alendronate, isopentenyl…”. X-ray diffraction, 4 ligands (AHD, IPE, MG), 11 pockets (best druggability 0.81). MolNFT…
- PDB
- 1YHM
- 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
- Q8WS26
- Ligands
- AHD, IPE, MG, SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 362 | 74% helix, 1% strand | Q8WS26 |
Ligands and binding sites
- AHD · 4-amino-1-hydroxybutane-1,1-diyldiphosphonate · 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 · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.81 | 0.93 | 47 | MG, AHD, IPE |
| 2 | 268 | 0.81 | 0.93 | 46 | MG, AHD, IPE |
| 3 | 292 | 0.81 | 0.92 | 46 | MG, AHD, IPE |
| 4 | 90 | 0.78 | 0.99 | 21 | empty |
| 5 | 221 | 0.51 | 0.76 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3167 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 346 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 45 modified (engineered).
Compared structures
- 1YHM · Structure of the complex of Trypanosoma cruzi farnesyl disphosphate synthase 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 Q8WS26
- Elsewhere: RCSB PDB 1YHM · PDBe 1YHM · UniProt Q8WS26
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