MolNFT v1 · #47139 · protein
Human farnesyl diphosphate synthase complexed with bisphosphonate bph- 461
2OPM · Farnesyl pyrophosphate synthetase (fpp synthetase) (fps)…: “Human farnesyl diphosphate synthase complexed with bisphosphonate bph- 461”. X-ray diffraction, 3 ligands (NI9, MG, PO4), 2 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 2OPM
- Type
- protein
- Length
- 336 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate…
- EC
- 2.5.1.10
- UniProt
- P14324
- Ligands
- NI9, MG, PO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltranstransferase (ec 2.5.1.1) (EC 2.5.1.10) | protein | 336 | 74% helix, 1% strand | P14324 |
Ligands and binding sites
- NI9 · 3-fluoro-1-(2-hydroxy-2,2-diphosphonoethyl)pyridinium · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.78 | 0.85 | 70 | PO4, MG, NI9 |
| 2 | 68 | 0.50 | 0.85 | 16 | empty |
Compared structures
- 2OPM · Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461 · the same entry in another collection · chain A against A, TM-score 1.00
- P14324 · AlphaFold monomer V2.0 prediction for farnesyl pyrophosphate synthase (P14324) · a predicted model of the same protein · 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 P14324
- Elsewhere: RCSB PDB 2OPM · PDBe 2OPM · UniProt P14324
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