Structure of PDB 6omb Chain E Binding Site BS02

Receptor Information
>6omb Chain E (length=536) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTG
KTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAI
IFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRP
NSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALA
AETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMD
NFRFALGNSVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSK
GVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDI
FDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMN
AKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLR
KTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAE
AMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNF
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 chain6omb Chain D Residue 904 [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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PDB6omb Structure of the Cdc48 segregase in the act of unfolding an authentic substrate.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		D343 R369
Binding residue
(residue number reindexed from 1)		D133 R159
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:0019888 protein phosphatase regulator activity
GO:0031593 polyubiquitin modification-dependent protein binding
GO:0042802 identical protein binding
GO:0043130 ubiquitin binding
Biological Process
GO:0006274 DNA replication termination
GO:0006515 protein quality control for misfolded or incompletely synthesized proteins
GO:0010636 positive regulation of mitochondrial fusion
GO:0015031 protein transport
GO:0016236 macroautophagy
GO:0016320 endoplasmic reticulum membrane fusion
GO:0030970 retrograde protein transport, ER to cytosol
GO:0031134 sister chromatid biorientation
GO:0032984 protein-containing complex disassembly
GO:0034517 ribophagy
GO:0034727 piecemeal microautophagy of the nucleus
GO:0036503 ERAD pathway
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043328 protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
GO:0046034 ATP metabolic process
GO:0051228 mitotic spindle disassembly
GO:0070651 nonfunctional rRNA decay
GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system
GO:0071630 nuclear protein quality control by the ubiquitin-proteasome system
GO:0072344 rescue of stalled ribosome
GO:0072671 mitochondria-associated ubiquitin-dependent protein catabolic process
GO:0097352 autophagosome maturation
GO:0099638 endosome to plasma membrane protein transport
GO:0120174 stress-induced homeostatically regulated protein degradation pathway
GO:1900182 positive regulation of protein localization to nucleus
GO:1902979 mitotic DNA replication termination
GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process
GO:1990171 SCF complex disassembly in response to cadmium stress
Cellular Component
GO:0000837 Doa10p ubiquitin ligase complex
GO:0000839 Hrd1p ubiquitin ligase ERAD-L complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0030894 replisome
GO:0034098 VCP-NPL4-UFD1 AAA ATPase complex
GO:0036266 Cdc48p-Npl4p-Vms1p AAA ATPase complex
GO:0043332 mating projection tip
GO:1990112 RQC complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6omb, PDBe:6omb, PDBj:6omb
PDBsum6omb
PubMed31249134
UniProtP25694|CDC48_YEAST Cell division control protein 48 (Gene Name=CDC48)

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