MolNFT v1 · #106378 · protein
T. brucei farnesyl diphosphate synthase complexed with risedronate
4RXD · Farnesyl pyrophosphate synthase: “T. brucei farnesyl diphosphate synthase complexed with risedronate”. X-ray diffraction, 2 ligands (RIS, MG), 14 pockets (best druggability 0.83). MolNFT v1 #106378 on GenesisL1: 3D structure…
- PDB
- 4RXD
- Type
- protein
- Length
- 1,069 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- UniProt
- Q86C09
- Ligands
- RIS, MG
- Pockets
- 14 · 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 | protein | 355 | 74% helix, 1% strand | Q86C09 |
| B, C | Farnesyl pyrophosphate synthase | protein | 357 | 74% helix, 1% strand | Q86C09 |
Ligands and binding sites
- RIS · 1-hydroxy-2-(3-pyridinyl)ethylidene bis-phosphonic acid · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.83 | 0.91 | 56 | MG, RIS |
| 2 | 379 | 0.81 | 0.90 | 54 | MG, RIS |
| 3 | 383 | 0.80 | 0.90 | 51 | RIS, MG |
| 4 | 57 | 0.52 | 0.87 | 15 | empty |
| 5 | 59 | 0.48 | 0.85 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 3211 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 438 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4RXD · T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate · 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 4RXD · PDBe 4RXD · UniProt Q86C09
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