Research workbench
Crystal structure of human fpps in complex with nickel, JDS05120, and sulfate
Analyse Crystal structure of human fpps in complex with nickel, JDS05120, and sulfate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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