Research workbench
T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-597
Analyse T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-597 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AEL
- Type
- protein
- Length
- 714 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
- QAF, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 357 | 74% helix, 1% strand | Q86C09 |
Ligands and binding sites
- QAF · {2-[3-(hex-1-yn-1-yl)pyridinium-1-yl]ethane-1,1-diyl}bis(phosphonate) · 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.83 | 0.90 | 60 | QAF, MG |
| 2 | 403 | 0.82 | 0.90 | 53 | QAF, MG |
| 3 | 132 | 0.45 | 0.77 | 17 | empty |
| 4 | 104 | 0.44 | 0.78 | 14 | empty |
| 5 | 57 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3277 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5AEL · T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-597 · 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 5AEL · PDBe 5AEL · UniProt Q86C09
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