Structure of PDB 2zan Chain A Binding Site BS02

Receptor Information
>2zan Chain A (length=312) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLF
GPPGTGKSYLAKAVATEANNSTFFSISSSSEKLVKNLFQLARENKPSIIF
IDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPW
VLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRK
TDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLT
PCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLK
LKKFTEDFGQEG
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 chain2zan Chain A Residue 446 [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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PDB2zan Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B
Resolution3.0 Å
Binding residue
(original residue number in PDB)		V136 A137 P176 G177 G179 K180 S181 Y182 N279 M309 H313 G338 S342
Binding residue
(residue number reindexed from 1)		V13 A14 P53 G54 G56 K57 S58 Y59 N147 M177 H181 G206 S210
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.6: vesicle-fusing ATPase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0044877 protein-containing complex binding
Biological Process
GO:0001525 angiogenesis
GO:0001778 plasma membrane repair
GO:0006813 potassium ion transport
GO:0006914 autophagy
GO:0006997 nucleus organization
GO:0007032 endosome organization
GO:0007034 vacuolar transport
GO:0007080 mitotic metaphase chromosome alignment
GO:0007417 central nervous system development
GO:0010824 regulation of centrosome duplication
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0015031 protein transport
GO:0016197 endosomal transport
GO:0030301 cholesterol transport
GO:0031468 nuclear membrane reassembly
GO:0032510 endosome to lysosome transport via multivesicular body sorting pathway
GO:0033993 response to lipid
GO:0036258 multivesicular body assembly
GO:0039702 viral budding via host ESCRT complex
GO:0043162 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
GO:0046761 viral budding from plasma membrane
GO:0051261 protein depolymerization
GO:0051301 cell division
GO:0060070 canonical Wnt signaling pathway
GO:0060856 establishment of blood-brain barrier
GO:0061738 late endosomal microautophagy
GO:0061764 late endosome to lysosome transport via multivesicular body sorting pathway
GO:0061952 midbody abscission
GO:0071985 multivesicular body sorting pathway
GO:0090148 membrane fission
GO:0090611 ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway
GO:0097352 autophagosome maturation
GO:1901673 regulation of mitotic spindle assembly
GO:1903542 negative regulation of exosomal secretion
GO:1903543 positive regulation of exosomal secretion
GO:1903724 positive regulation of centriole elongation
GO:1904903 ESCRT III complex disassembly
Cellular Component
GO:0000922 spindle pole
GO:0005634 nucleus
GO:0005643 nuclear pore
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030496 midbody
GO:0031902 late endosome membrane
GO:0090543 Flemming body
GO:1904949 ATPase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2zan, PDBe:2zan, PDBj:2zan
PDBsum2zan
PubMed18796009
UniProtP46467|VPS4B_MOUSE Vacuolar protein sorting-associated protein 4B (Gene Name=Vps4b)

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