Research workbench
Trypanosoma cruzi farnesyl diphosphate synthase homodimer in complex with minodronate and isopentenyl disphosphate
Analyse Trypanosoma cruzi farnesyl diphosphate synthase homodimer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ICK
- Type
- protein
- Length
- 362 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.10
- UniProt
- Q95WL3
- Ligands
- M0N, IPE, MG, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 362 | 75% helix, 2% strand | Q95WL3 |
Ligands and binding sites
- M0N · (1-hydroxy-2-imidazo[1,2-a]pyridin-3-ylethane-1,1-diyl)bis(phosphonic acid) · ligand · chains A
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.81 | 0.92 | 47 | M0N, SO4, IPE, MG |
| 2 | 50 | 0.54 | 0.89 | 15 | ACY |
| 3 | 65 | 0.33 | 0.75 | 15 | empty |
| 4 | 59 | 0.31 | 0.75 | 12 | empty |
Compared structures
- 3ICK · Trypanosoma cruzi farnesyl diphosphate synthase homodimer in complex with minodronate and… · 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 3ICK · PDBe 3ICK · UniProt Q95WL3
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