MolNFT v1 · #106379 · protein
T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-14
4RXE · Farnesyl pyrophosphate synthase: “T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-14”. X-ray diffraction, 2 ligands (3YQ, MG), 9 pockets (best druggability 0.82). MolNFT v1 #106379 on GenesisL1: 3D…
- PDB
- 4RXE
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- UniProt
- Q86C09
- Ligands
- 3YQ, MG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase | protein | 358 | 72% helix, 1% strand | Q86C09 |
| B | Farnesyl pyrophosphate synthase | protein | 359 | 73% helix, 1% strand | Q86C09 |
Ligands and binding sites
- 3YQ · {[(3-methylpyridin-2-yl)amino]methanediyl}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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.82 | 0.91 | 54 | 3YQ, MG |
| 2 | 398 | 0.80 | 0.89 | 50 | 3YQ, MG |
| 3 | 114 | 0.65 | 0.88 | 25 | empty |
| 4 | 52 | 0.50 | 0.87 | 16 | empty |
| 5 | 105 | 0.46 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3159 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 4RXE · T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-14 · 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 4RXE · PDBe 4RXE · UniProt Q86C09
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