Structure of PDB 6ndy Chain B Binding Site BS03

Receptor Information
>6ndy Chain B (length=322) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKKLRGALSSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG
NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESE
KLVKQLFAMARENKPSIIFIDEVDALTGTRGEGESEASRRIKTELLVQMN
GVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEIN
VGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFK
DVSETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRP
TVNEDDLLKQEQFTRDFGQEGN
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 chain6ndy Chain B Residue 501 [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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PDB6ndy Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		G176 T177 K179 S180 Y181 G336
Binding residue
(residue number reindexed from 1)		G65 T66 K68 S69 Y70 G225
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity

View graph for
Molecular Function
External links
PDB RCSB:6ndy, PDBe:6ndy, PDBj:6ndy
PDBsum6ndy
PubMed31184588
UniProtP52917|VPS4_YEAST Vacuolar protein sorting-associated protein 4 (Gene Name=VPS4)

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