Research workbench
T. brucei farnesyl diphosphate synthase complexed with bisphosphonate
Analyse T. brucei farnesyl diphosphate synthase complexed with bisphosphonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I19
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.10
- UniProt
- Q86C09
- Ligands
- 1BY, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 367 | 71% helix, 1% strand | Q86C09 |
| B | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 361 | 73% helix, 1% strand | Q86C09 |
Ligands and binding sites
- 1BY · [2-(pyridin-2-ylamino)ethane-1,1-diyl]bis(phosphonic acid) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.82 | 0.85 | 69 | MG, 1BY |
| 2 | 547 | 0.82 | 0.88 | 61 | MG, 1BY |
| 3 | 88 | 0.52 | 0.83 | 22 | empty |
| 4 | 146 | 0.50 | 0.79 | 24 | empty |
| 5 | 81 | 0.43 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3244 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 2I19 · T. Brucei farnesyl diphosphate synthase complexed with bisphosphonate · 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 Q86C09
- Elsewhere: RCSB PDB 2I19 · PDBe 2I19 · UniProt Q86C09
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