MolNFT v1 · #101050 · protein
Crystal structure of human fpps in complex with nickel, JDS05120, and sulfate
4NFK · Farnesyl pyrophosphate synthase: “Crystal structure of human fpps in complex with nickel, JDS05120, and sulfate”. X-ray diffraction, 3 ligands (JD5, NI, SO4), 1 pocket (best druggability 0.79). MolNFT v1 #101050 on GenesisL1: 3D…
- PDB
- 4NFK
- Type
- protein
- Length
- 342 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
- JD5, NI, SO4
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Farnesyl pyrophosphate synthase (EC 2.5.1.10, 2.5.1.1) | protein | 342 | 77% helix, 1% strand | P14324 |
Ligands and binding sites
- JD5 · [({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid) · ligand · chains F
- NI · Nickel (II) ion · metal · 3 copies · chains F
- SO4 · Sulfate ion · ion · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.79 | 0.85 | 62 | NI, JD5, SO4 |
Compared structures
- 4NFK · Crystal structure of human FPPS in complex with nickel, JDS05120, and sulfate · the same entry in another collection · chain F against F, TM-score 1.00
- P14324 · AlphaFold monomer V2.0 prediction for farnesyl pyrophosphate synthase (P14324) · a predicted model of the same protein · chain F 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 4NFK · PDBe 4NFK · UniProt P14324
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