Structure of PDB 6omb Chain E

Receptor sequence
>6ombE (length=536) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
VGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTG
KTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAI
IFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRP
NSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALA
AETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMD
NFRFALGNSVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSK
GVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDI
FDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMN
AKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLR
KTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAE
AMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNF
3D structure
PDB6omb Structure of the Cdc48 segregase in the act of unfolding an authentic substrate.
ChainE
Resolution3.7 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.6.4.6: vesicle-fusing ATPase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 peptide E M560 W561 Y562 M338 W339 Y340
BS02 ADP E D343 R369 D133 R159
BS03 ADP E G490 P530 G531 T532 G533 K534 T535 I666 Q670 G694 L698 G268 P308 G309 T310 G311 K312 T313 I444 Q448 G472 L476
BS04 ADP E D215 G217 G258 T259 G260 T262 L263 H394 A419 D5 G7 G48 T49 G50 T52 L53 H184 A209
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:6omb, PDBe:6omb, PDBj:6omb
PDBsum6omb
PubMed31249134
UniProtP25694|CDC48_YEAST Cell division control protein 48 (Gene Name=CDC48)

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