Structure of PDB 5xmk Chain E Binding Site BS02

Receptor Information
>5xmk Chain E (length=319) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSG
ILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLF
AMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQ
GVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCV
LTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDD
ETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVN
EDDLLKQEQFTRDFGQEGN
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain5xmk Chain F 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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PDB5xmk Cryo-EM structures of the ATP-bound Vps4(E233Q) hexamer and its complex with Vta1 at near-atomic resolution
Resolution4.18 Å
Binding residue
(original residue number in PDB)		N265 R289
Binding residue
(residue number reindexed from 1)		N147 R171
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:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0001778 plasma membrane repair
GO:0006914 autophagy
GO:0006997 nucleus organization
GO:0007033 vacuole organization
GO:0015031 protein transport
GO:0016125 sterol metabolic process
GO:0016197 endosomal transport
GO:0016236 macroautophagy
GO:0031468 nuclear membrane reassembly
GO:0032511 late endosome to vacuole transport via multivesicular body sorting pathway
GO:0036258 multivesicular body assembly
GO:0045053 protein retention in Golgi apparatus
GO:0045324 late endosome to vacuole transport
GO:0061709 reticulophagy
GO:0061764 late endosome to lysosome transport via multivesicular body sorting pathway
GO:0061952 midbody abscission
GO:0070676 intralumenal vesicle formation
GO:0071985 multivesicular body sorting pathway
GO:0090148 membrane fission
GO:0097352 autophagosome maturation
Cellular Component
GO:0005643 nuclear pore
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030496 midbody
GO:1904949 ATPase complex
GO:1990621 ESCRT IV complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5xmk, PDBe:5xmk, PDBj:5xmk
PDBsum5xmk
PubMed28714467
UniProtP52917|VPS4_YEAST Vacuolar protein sorting-associated protein 4 (Gene Name=VPS4)

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