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Crystal structure of human fpps in complex with zoledronate and isopentenyl diphosphate

Analyse Crystal structure of human fpps in complex with zoledronate and isopentenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2F8Z
Type
protein
Length
346 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Farnesyl diphosphate synthase
EC
2.5.1.1, 2.5.1.10
UniProt
P14324
Ligands
IPE, ZOL, MG
Pockets
1 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 72% helix, 1% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
FFarnesyl diphosphate synthase (EC 2.5.1.1, 2.5.1.10)protein34672% helix, 1% strandP14324

Ligands and binding sites

  • IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains F
  • ZOL · Zoledronic acid · ligand · chains F
  • MG · Magnesium ion · metal · 3 copies · 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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12850.820.9346MG, IPE, ZOL

Compared structures

  • 2F8Z · Crystal structure of human FPPS in complex with zoledronate and isopentenyl diphosphate · 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 0.99

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