Research workbench
Crystal structure of human fpps in complex with salicylic acid derivative 3A
Analyse Crystal structure of human fpps in complex with salicylic acid derivative 3A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DIQ
- Type
- protein
- Length
- 345 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
- 5B9, MG, PO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 75% 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 | 345 | 75% helix, 1% strand | P14324 |
Ligands and binding sites
- 5B9 · 2-(naphthalen-1-ylmethoxy)benzoic acid · ligand · chains F
- MG · Magnesium ion · metal · chains F
- PO4 · Phosphate ion · ion · chains F
- GOL · Glycerol · additive · 2 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.77 | 0.79 | 82 | GOL, 5B9, MG, PO4 |
| 2 | 60 | 0.33 | 0.76 | 16 | empty |
| 3 | 59 | 0.30 | 0.75 | 14 | empty |
Compared structures
- 5DIQ · Crystal structure of human FPPS in complex with salicylic acid derivative 3a · 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 0.96
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 5DIQ · PDBe 5DIQ · UniProt P14324
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