Structure of PDB 6opc Chain A Binding Site BS03

Receptor Information
>6opc Chain A (length=733) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLI
VLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIA
DTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMV
ELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLIN
GPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIG
IPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAM
QQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPP
GTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAA
PTVVFLDELDSIAKARGGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGAT
NRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELT
AIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVP
YITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM
Ligand information
Ligand IDBEF
InChIInChI=1S/Be.3FH/h;3*1H/q+2;;;/p-3
InChIKeyOGIAHMCCNXDTIE-UHFFFAOYSA-K
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[Be-](F)(F)F
ACDLabs 10.04
CACTVS 3.341		F[Be-](F)F
FormulaBe F3
NameBERYLLIUM TRIFLUORIDE ION
ChEMBL
DrugBank
ZINC
PDB chain6opc Chain A Residue 902 [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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PDB6opc Structure of the Cdc48 segregase in the act of unfolding an authentic substrate.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		P530 K534 N634
Binding residue
(residue number reindexed from 1)		P500 K504 N601
Annotation score1
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6opc, PDBe:6opc, PDBj:6opc
PDBsum6opc
PubMed31249134
UniProtP25694|CDC48_YEAST Cell division control protein 48 (Gene Name=CDC48)

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