Structure of PDB 5ygi Chain A

Receptor sequence
>5ygiA (length=338) Species: 9606 (Homo sapiens) [Search protein sequence]
DVYAQEKQDFVQHFSQIVRVLTEHPEIGDAIARLKEVLEYNAIGGKYNRG
LTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLT
RRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFL
QSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIA
AAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTD
IQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLP
AVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIY
3D structure
PDB5ygi The Mevalonate Pathway Is a Druggable Target for Vaccine Adjuvant Discovery.
ChainA
Resolution2.177 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) K57 F98 D103 D107 R112 D174 K200 F239 D243 D244
Catalytic site (residue number reindexed from 1) K46 F87 D92 D96 R101 D163 K189 F228 D232 D233
Enzyme Commision number 2.5.1.1: dimethylallyltranstransferase.
2.5.1.10: (2E,6E)-farnesyl diphosphate synthase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MG A D103 D107 D92 D96
BS02 MG A D103 D107 D92 D96
BS03 T93 A F98 F99 D103 M106 R112 Q171 K200 D243 K257 F87 F88 D92 M95 R101 Q160 K189 D232 K246 PDBbind-CN: -logKd/Ki=7.05,IC50=90nM
Gene Ontology
Molecular Function
GO:0004659 prenyltransferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
Biological Process
GO:0008299 isoprenoid biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:5ygi, PDBe:5ygi, PDBj:5ygi
PDBsum5ygi
PubMed30270039
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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