Structure of PDB 6ap1 Chain E Binding Site BS01

Receptor Information
>6ap1 Chain E (length=304) Species: 208964,559292 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPP
GTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENK
PSIIFIDEVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGA
TNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYR
TLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSETRKLTPCSPG
DDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFT
RDFG
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 chain6ap1 Chain E Residue 701 [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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PDB6ap1 The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		P175 G176 G178 K179 Y181 M307 G336
Binding residue
(residue number reindexed from 1)		P50 G51 G53 K54 Y56 M182 G211
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
Cellular Component
GO:0005576 extracellular region

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:6ap1, PDBe:6ap1, PDBj:6ap1
PDBsum6ap1
PubMed29165244
UniProtP52917|VPS4_YEAST Vacuolar protein sorting-associated protein 4 (Gene Name=VPS4);
Q9I747

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