Structure of PDB 6oab Chain D Binding Site BS03

Receptor Information

>6oab Chain D (length=537) Species: 4932 (Saccharomyces cerevisiae)

NEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPG
TGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAP
AIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATN
RPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEA
LAAETHGYVGADIASLCSEAAMQQIREKMLGVTMDNFRFALGNSNPSALR
ETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVL
FYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDK
ARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKK
NVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTP
LEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRVDPVPYIT
KEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQF

Ligand information

• Ligand ID: BEF
• InChI: InChI=1S/Be.3FH/h;3*1H/q+2;;;/p-3
• InChIKey: OGIAHMCCNXDTIE-UHFFFAOYSA-K
• SMILES:
  OpenEye OEToolkits 1.5.0: [Be-](F)(F)F
  ACDLabs 10.04
  CACTVS 3.341: F[Be-](F)F
• Formula: Be F3
• Name: BERYLLIUM TRIFLUORIDE ION
• PDB chain: 6oab Chain D Residue 903

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6oab Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): K534 T535 E588 A632
• Binding residue (residue number reindexed from 1): K309 T310 E363 A407
• Annotation score: 1

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

External links

• PDB: RCSB:6oab, PDBe:6oab, PDBj:6oab
• PDBsum: 6oab
• PubMed: 31249135
• UniProt: P25694|CDC48_YEAST Cell division control protein 48 (Gene Name=CDC48)