Structure of PDB 8dnc Chain A Binding Site BS03

Receptor Information
>8dnc Chain A (length=395) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIRVFDVWKKYKYYKKPQDRLKEIIFRKPFHEELWVLKGINLEIEKGEVL
GIVGPNGAGKSTLLKVITGVTEPDKGFVERSGKVVGLLELGTGFNYELSG
LENIYVNASLLGLSRREIDEKLESIIEFSELDDFINKPLKTYSSGMIMRL
AFSIAIHTEPECFIIDEALAVGDAHFQQKCFRKLKEHKQKGGSIIFVSHD
MNAVKILCDRAILLHKGEIIEEGSPETVTQAYYKLMASLENKEGITFLQN
GYGNFKAVIKEVRLKSEHGYTNNFPSGDTLFIELDVEAKEDLQDVVAGIL
IRDRFGQDIFGINTYLMEKKVELKKGKYLFTFKMPLNLAPGKYTLTVALH
KGMDHAQECYHWIDNVCNFEVNGFKKEQFVGVCYLPTEFNYRKIP
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 chain8dnc Chain A Residue 502 [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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PDB8dnc Molecular basis for polysaccharide recognition and modulated ATP hydrolysis by the O antigen ABC transporter.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		Y11 Y13 G57 G59 K60 S61
Binding residue
(residue number reindexed from 1)		Y11 Y13 G57 G59 K60 S61
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0140359 ABC-type transporter activity
Biological Process
GO:0055085 transmembrane transport
Cellular Component
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:8dnc, PDBe:8dnc, PDBj:8dnc
PDBsum8dnc
PubMed36064941
UniProtO67181

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