Structure of PDB 5nbd Chain A Binding Site BS01

Receptor Information
>5nbd Chain A (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 A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		G385 K388 S389
Binding residue
(residue number reindexed from 1)		G385 K388 S389
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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