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Crystal structure of human fpps in ternary complex with YS0470 and isopentenyl pyrophosphate

Analyse Crystal structure of human fpps in ternary complex with YS0470 and isopentenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4H5E
Type
protein
Length
346 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Farnesyl pyrophosphate synthase
EC
2.5.1.1, 2.5.1.10
UniProt
P14324
Ligands
YS4, IPR, MG
Pockets
1 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
FFarnesyl pyrophosphate synthase (EC 2.5.1.1, 2.5.1.10)protein34676% helix, 1% strandP14324

Ligands and binding sites

  • YS4 · [({4-[4-(propan-2-yloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid) · ligand · chains F
  • IPR · Isopentyl pyrophosphate · 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
13330.800.9055YS4, IPR, MG

Compared structures

  • 4H5E · Crystal structure of human FPPS in ternary complex with YS0470 and isopentenyl… · 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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