2K8C

Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2k8ca_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PFU(mutate) domain-like	8055783	3002311	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ubiquitin_1	e2k8cA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	PFU	e2k8cB1	A: a+b two layers	X: ubiquitin-binding domain from PLAA (From Topology)	H: ubiquitin-binding domain from PLAA (From Topology)	T: ubiquitin-binding domain from PLAA	F: PFU	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.870	Alpha Beta	Roll	Ubiquitin-like (UB roll)	PFU (PLAA family ubiquitin binding), C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
B	PF09070	PFU (PLAA family ubiquitin binding) (PFU)	PFU (PLAA family ubiquitin binding)	This domain is found N terminal to Pfam:PF08324 and binds to ubiquitin [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding organic cyclic compound binding nucleic acid binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B	Phospholipase A-2-activating protein	protein binding binding ubiquitin binding ubiquitin-like protein binding enzyme regulator activity phospholipase A2 activator activity enzyme activator activity molecular function activator activity phospholipase activator activity molecular function regulator activity lipase activator activity	regulation of localization cellular localization regulation of biological process transport regulation of transport positive regulation of synaptic vesicle recycling synaptic vesicle cycle biological regulation positive regulation of biological process regulation of synaptic vesicle recycling establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse synaptic vesicle recycling localization regulation of localization cellular localization regulation of biological process transport regulation of transport positive regulation of synaptic vesicle recycling synaptic vesicle cycle biological regulation positive regulation of biological process regulation of synaptic vesicle recycling establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse synaptic vesicle recycling localization positive regulation of transport establishment of localization in cell cellular process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process primary metabolic process phosphorus metabolic process lipid metabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process protein metabolic process macromolecule metabolic process multicellular organismal process positive regulation of locomotion regulation of cell motility regulation of cellular process cellular developmental process regulation of neuron migration positive regulation of cell migration neurogenesis multicellular organism development cell differentiation positive regulation of cell motility anatomical structure development regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process system development developmental process neuron migration nervous system development generation of neurons regulation of locomotion positive regulation of neuron migration negative regulation of post-translational protein modification regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process protein K63-linked ubiquitination regulation of protein K63-linked ubiquitination protein ubiquitination negative regulation of protein modification process negative regulation of cellular process protein modification process regulation of protein modification by small protein conjugation or removal negative regulation of protein ubiquitination negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of protein K63-linked ubiquitination regulation of protein polyubiquitination negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process protein polyubiquitination regulation of macromolecule metabolic process negative regulation of protein polyubiquitination macromolecule modification post-translational protein modification protein modification by small protein conjugation regulation of metabolic process protein modification by small protein conjugation or removal prostaglandin metabolic process icosanoid metabolic process fatty acid metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process prostanoid metabolic process small molecule metabolic process monocarboxylic acid metabolic process cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to stimulus response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of phospholipase activity positive regulation of phospholipase activity regulation of catalytic activity positive regulation of catalytic activity positive regulation of lipase activity positive regulation of phospholipase A2 activity regulation of phospholipase A2 activity regulation of molecular function positive regulation of molecular function positive regulation of hydrolase activity regulation of hydrolase activity regulation of lipase activity signaling signal transduction cell communication proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macroautophagy autophagy process utilizing autophagic mechanism cellular homeostasis homeostatic process ubiquitin recycling defense response response to stress inflammatory response regulation of growth developmental growth cell projection organization neuron projection development regulation of cell morphogenesis positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis positive regulation of developmental growth developmental growth involved in morphogenesis positive regulation of dendrite extension regulation of cellular component organization regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis cellular component organization cellular component organization or biogenesis dendrite extension regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth anatomical structure morphogenesis positive regulation of growth neuron development	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm synapse cell junction extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm synapse cell junction intracellular organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR019954	Ubiquitin conserved site	Conserved Site
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR019956	Ubiquitin domain	Domain
A	IPR050158	Ubiquitin and ubiquitin-like	Family
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR016024	Armadillo-type fold	Homologous Superfamily
B	IPR015155	PLAA family ubiquitin binding domain	Domain
B	IPR011989	Armadillo-like helical	Homologous Superfamily
B	IPR013535	PUL domain	Domain
B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B	IPR038122	PFU domain superfamily	Homologous Superfamily
B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B	IPR001680	WD40 repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer
B	Pharos: Q9Y263	Inflammation neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies medulloblastoma ovarian cancer intellectual disability osteosarcoma schizophrenia

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.