MolNFT v1 · #62481 · protein
T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-722
3EGT · Farnesyl pyrophosphate synthase: “T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-722”. X-ray diffraction, 2 ligands (722, MG), 8 pockets (best druggability 0.83). MolNFT v1 #62481 on GenesisL1: 3D…
- PDB
- 3EGT
- Type
- protein
- Length
- 717 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
- 722, MG
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 358 | 74% helix, 1% strand | Q86C09 |
| B | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 359 | 74% helix, 1% strand | Q86C09 |
Ligands and binding sites
- 722 · 1-(2,2-diphosphonoethyl)-3-(heptyloxy)pyridinium · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.83 | 0.92 | 58 | MG, 722 |
| 2 | 330 | 0.81 | 0.91 | 51 | MG, 722 |
| 3 | 99 | 0.76 | 0.97 | 27 | empty |
| 4 | 50 | 0.47 | 0.86 | 20 | empty |
| 5 | 115 | 0.46 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3093 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 3EGT · T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-722 · 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 3EGT · PDBe 3EGT · UniProt Q86C09
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