Research workbench
T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-210
Analyse T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-210 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P1C
- 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
- GG3, MG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 357 | 73% helix, 2% strand | Q86C09 |
Ligands and binding sites
- GG3 · {1-hydroxy-3-[methyl(4-phenylbutyl)amino]propane-1,1-diyl}bis(phosphonic acid) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · chains 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 | 463 | 0.83 | 0.90 | 58 | MG, ACT, GG3 |
| 2 | 501 | 0.83 | 0.89 | 57 | MG, ACT, GG3 |
| 3 | 64 | 0.58 | 0.89 | 18 | empty |
| 4 | 77 | 0.56 | 0.87 | 20 | empty |
| 5 | 52 | 0.49 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3165 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2P1C · T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-210 · 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 2P1C · PDBe 2P1C · UniProt Q86C09
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