Structure of PDB 5xmi Chain D Binding Site BS01

Receptor Information
>5xmi Chain D (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 chain5xmi Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5xmi Cryo-EM structures of the ATP-bound Vps4(E233Q) hexamer and its complex with Vta1 at near-atomic resolution
Resolution3.9 Å
Binding residue
(original residue number in PDB)		G176 T177 G178 K179 S180 Y181 N277 M307 G336
Binding residue
(residue number reindexed from 1)		G58 T59 G60 K61 S62 Y63 N159 M189 G218
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5xmi, PDBe:5xmi, PDBj:5xmi
PDBsum5xmi
PubMed28714467
UniProtP52917|VPS4_YEAST Vacuolar protein sorting-associated protein 4 (Gene Name=VPS4)

[Back to BioLiP]