Structure of PDB 2zao Chain A Binding Site BS01
Receptor Information
>2zao Chain A (length=312) Species:
10090
(Mus musculus) [
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IVIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLF
GPPGTGKSYLAKAVATEANNSTFFSISSSSEKLVKNLFQLARENKPSIIF
IDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPW
VLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRK
TDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLT
PCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLK
LKKFTEDFGQEG
Ligand information
Ligand ID
ADP
InChI
InChI=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
InChIKey
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(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 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Formula
C10 H15 N5 O10 P2
Name
ADENOSINE-5'-DIPHOSPHATE
ChEMBL
CHEMBL14830
DrugBank
DB16833
ZINC
ZINC000012360703
PDB chain
2zao Chain A Residue 445 [
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Receptor-Ligand Complex Structure
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PDB
2zao
Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B
Resolution
3.2 Å
Binding residue
(original residue number in PDB)
A137 P176 G177 T178 G179 K180 S181 Y182 M309 H313 G338 S342
Binding residue
(residue number reindexed from 1)
A14 P53 G54 T55 G56 K57 S58 Y59 M177 H181 G206 S210
Annotation score
5
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
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Cellular Component
External links
PDB
RCSB:2zao
,
PDBe:2zao
,
PDBj:2zao
PDBsum
2zao
PubMed
18796009
UniProt
P46467
|VPS4B_MOUSE Vacuolar protein sorting-associated protein 4B (Gene Name=Vps4b)
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