Research workbench
Human farnesyl diphosphate synthase in complex with arenarone and zoledronate
Analyse Human farnesyl diphosphate synthase in complex with arenarone and zoledronate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P0W
- Type
- protein
- Length
- 346 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.10, 2.5.1.1
- UniProt
- P14324
- Ligands
- 1XH, ZOL, MG
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase (EC 2.5.1.10, 2.5.1.1) | protein | 346 | 75% helix, 1% strand | P14324 |
Ligands and binding sites
- 1XH · 2-{[(1S,2R,4aS,8aR)-1,2,4a-trimethyl-5-methylidenedecahydronaphthalen-1-yl]methyl}cyclohexa-2,5-diene-1,4-dione · ligand · chains A
- ZOL · Zoledronic acid · ligand · chains A
- MG · Magnesium ion · metal · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.83 | 0.93 | 54 | 1XH, ZOL, MG |
| 2 | 50 | 0.29 | 0.75 | 16 | empty |
Compared structures
- 4P0W · Human farnesyl diphosphate synthase in complex with Arenarone and zoledronate · 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 0.99
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 4P0W · PDBe 4P0W · UniProt P14324
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