Structure of PDB 8xkf Chain B

Receptor sequence

>8xkfB (length=362) Species: 85962 (Helicobacter pylori 26695)

HHIKQTSVVLLAAGESRRFSQTIKKQWLRSNHTPLWLSVYESFKEALDFK
EIILVVSELDYIYIKRHYPEIKLVKGGASRQESVRNALKIIDSAYTLTSD
VARGLANIEALKNLFLTLQQTSHYCIAPYLPCYDTAIYYNEALDREAIKL
IQTPQLSHTKALQSALNQGDFKDESSAILQAFPDRVSYIEGSFTLFFNPA
KDTFIGMGFDTHAFIKDKPMVLGGVVLDCEFGLKAHSDGDALLHAVIDAI
LGAIKGGDIGEWFPDNDPKYKNASSKELLKIVLDFSQSIGFELFEMGATI
FSEIPKITPYKPAILENLSQLLGLEKSQISLKATTMEKMGFIGKQEGLLV
QAHVSMRYKQKL

3D structure

• PDB: 8xkf Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes.
• Chain: B
• 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	B	L41 A42 A43 G44 E45 S46 R47 R48 K55 G107 S109 R110 S113 D130	L11 A12 A13 G14 E15 S16 R17 R18 K25 G77 S79 R80 S83 D100
BS02	C5P	B	S346 P349 K350 I351 T352 A377 T378 T379	S302 P305 K306 I307 T308 A333 T334 T335

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)