Structure of PDB 8dav Chain F Binding Site BS01

Receptor Information
>8dav Chain F (length=551) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKRKRVVRNNLRIREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHP
QLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSK
MAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQ
LLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGR
LEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKM
DLIIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLD
EIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVAT
EVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIA
SDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVP
LPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAK
YAIKDSIEAHRQDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMK
A
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 chain8dav Chain F Residue 901 [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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PDB8dav SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		G217 G258 T259 G260 K261 T262 L263 G418
Binding residue
(residue number reindexed from 1)		G30 G71 T72 G73 K74 T75 L76 G231
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8dav, PDBe:8dav, PDBj:8dav
PDBsum8dav
PubMed36574706
UniProtP25694|CDC48_YEAST Cell division control protein 48 (Gene Name=CDC48)

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