Structure of PDB 8xkf Chain A

Receptor sequence

>8xkfA (length=370) Species: 85962 (Helicobacter pylori 26695)

HHHIKQTSVVLLAAGESRRFSQTIKKQWLRSNHTPLWLSVYESFKEALDF
KEIILVVSELDYIYIKRHYPEIKLVKGGASRQESVRNALKIIDSAYTLTS
DVARGLANIEALKNLFLTLQQTSHYCIAPYLPCYDTAIYYNEALDREAIK
LIQTPQLSHTKALQSALNQGDFKDESSAILQAFPDRVSYIEGSKLTTSGD
LFTLFFNPAKDTFIGMGFDTHAFIKDKPMVLGGVVLDCEFGLKAHSDGDA
LLHAVIDAILGAIKGGDIGEWFPDNDPKYKNASSKELLKIVLDFSQSIGF
ELFEMGATIFSEIPKITPYKPAILENLSQLLGLEKSQISLKATTMEKMGF
IGKQEGLLVQAHVSMRYKQK

3D structure

• PDB: 8xkf Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes.
• Chain: A
• Resolution: 2.5 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.60: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase.
  4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate 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	CTP	A	L41 A42 A43 G44 E45 S46 R47 R48 K55 S109 S113 D130 K227	L12 A13 A14 G15 E16 S17 R18 R19 K26 S80 S84 D101 K194
BS02	ZN	A	H256 H288	H221 H253
BS03	CDP	A	D302 G304	D267 G269

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0016829 lyase activity
• GO:0046872 metal ion binding
• GO:0050518 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
• GO:0070567 cytidylyltransferase activity

Biological Process

• GO:0008299 isoprenoid biosynthetic process
• GO:0016114 terpenoid biosynthetic process
• GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

External links

• PDB: RCSB:8xkf, PDBe:8xkf, PDBj:8xkf
• PDBsum: 8xkf
• PubMed: 38537721
• UniProt: O25664|ISPDF_HELPY Bifunctional enzyme IspD/IspF (Gene Name=ispDF)