Structure of PDB 8xkf Chain D

Receptor sequence
>8xkfD (length=375) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence]
HHIKQTSVVLLAAGESRRFSQTIKKQWLRSNHTPLWLSVYESFKEALDFK
EIILVVSELDYIYIKRHYPEIKLVKGGASRQESVRNALKIIDSAYTLTSD
VARGLANIEALKNLFLTLQQTSHYCIAPYLPCYDTAIYYNEALDREAIKL
IQTPQLSHTKALQSALNQGDFKDESSAILQAFPDRVSYIEGSKDLHKLTT
SGDLKHFTLFFNPAKDTFIGMGFDTHAFIKDKPMVLGGVVLDCEFGLKAH
SDGDALLHAVIDAILGAIKGGDIGEWFPDNDPKYKNASSKELLKIVLDFS
QSIGFELFEMGATIFSEIPKITPYKPAILENLSQLLGLEKSQISLKATTM
EKMGFIGKQEGLLVQAHVSMRYKQK
3D structure
PDB8xkf Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes.
ChainD
Resolution2.5 Å
3D
structure
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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 D L41 A42 A43 G44 E45 S46 R47 R48 K55 S109 R110 S113 D130 K227 L11 A12 A13 G14 E15 S16 R17 R18 K25 S79 R80 S83 D100 K197
BS02 C5P D S346 K350 I351 T352 A377 T378 T379 S316 K320 I321 T322 A347 T348 T349
BS03 ZN D D254 H256 H288 D224 H226 H258
BS04 CDP D D302 G304 D272 G274
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

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Molecular Function
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Biological Process
External links
PDB RCSB:8xkf, PDBe:8xkf, PDBj:8xkf
PDBsum8xkf
PubMed38537721
UniProtO25664|ISPDF_HELPY Bifunctional enzyme IspD/IspF (Gene Name=ispDF)

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