Structure of PDB 5nbd Chain B Binding Site BS01

Receptor Information
>5nbd Chain B (length=564) Species: 197 (Campylobacter jejuni) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVKKLFFILSKEDKNFLFFLLVFSVFVSFIETFAISLVMPFITLASDFSY
FDRNKYLISLKEYLNIPVFEIIVYFGVGLIVFYVFRALLNAYYFHLLARF
SKGRKHAIAYKVFSKFLNINYEKFTQKNQSEILKSITGEVYNLSTMISSF
LLLMSEIFVVLLLYALMLLINYKITLFLSIFMVLNAFILVKILSPIIKKA
GLRREEAMKNFFEILNTNLNNFKFIKLKTKEDGVLSLFKAQSEAFSKANI
TNESVAAVPRIYLEGIGFCVLVFIVVFLVLKNESDISGILSTISIFVLAL
YRLMPSANRIITSYHDLLYYHSSLNIIYQNLRQEEENLGEGKLSFNQELK
ICNLSFGYEGKKYLFKNLNLNIKKGEKIAFIGESGCGKSTLVDLIIGLLK
PKEGQILIDKQELNASNAKNYRQKIGYIPQNIYLFNDSIAKNITFGDAVD
EEKLNKVIKQANLEHFIKNLPQGVQTKVGDGGSNLSGGQKQRIAIARALY
LEPEILVLDQATSALDTQSEAKIMDEIYKISKDKTMIIIAHRLSTITQCD
KVYRLEHGKLKEEK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5nbd Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nbd Structural basis of inhibition of lipid-linked oligosaccharide flippase PglK by a conformational nanobody.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		T125 Y358 K361 G385 C386 G387 K388 S389 T390
Binding residue
(residue number reindexed from 1)		T125 Y358 K361 G385 C386 G387 K388 S389 T390
Annotation score5
Enzymatic activity
Enzyme Commision number 7.5.2.5: ABC-type lipopolysaccharide transporter.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0015437 lipopolysaccharide floppase activity
GO:0016887 ATP hydrolysis activity
GO:0034040 ATPase-coupled lipid transmembrane transporter activity
GO:0140359 ABC-type transporter activity
Biological Process
GO:0006486 protein glycosylation
GO:0006487 protein N-linked glycosylation
GO:0006869 lipid transport
GO:0015920 lipopolysaccharide transport
GO:0018279 protein N-linked glycosylation via asparagine
GO:0055085 transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nbd, PDBe:5nbd, PDBj:5nbd
PDBsum5nbd
PubMed28422165
UniProtQ0P9C4|PGLK_CAMJE Protein glycosylation K (Gene Name=pglK)

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