MolNFT v1 · #106377 · protein
T. brucei farnesyl diphosphate synthase complexed with homorisedronate bph-6
4RXC · Farnesyl pyrophosphate synthase: “T. brucei farnesyl diphosphate synthase complexed with homorisedronate bph-6”. X-ray diffraction, 2 ligands (HRX, MG), 7 pockets (best druggability 0.73). MolNFT v1 #106377 on GenesisL1: 3D…
- PDB
- 4RXC
- Type
- protein
- Length
- 703 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- UniProt
- Q86C09
- Ligands
- HRX, MG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase | protein | 351 | 74% helix, 1% strand | Q86C09 |
| B | Farnesyl pyrophosphate synthase | protein | 352 | 75% helix, 1% strand | Q86C09 |
Ligands and binding sites
- HRX · [1-hydroxy-3-(pyridin-3-yl)propane-1,1-diyl]bis(phosphonic acid) · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.73 | 0.78 | 71 | HRX, MG |
| 2 | 836 | 0.72 | 0.77 | 73 | HRX, MG |
| 3 | 55 | 0.52 | 0.88 | 15 | empty |
| 4 | 150 | 0.50 | 0.78 | 18 | empty |
| 5 | 52 | 0.49 | 0.87 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3406 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 4RXC · T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate BPH-6 · 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 4RXC · PDBe 4RXC · UniProt Q86C09
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