6YPT | pdb_00006ypt

X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8105553	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8105553	3001808	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)
D	Pro_isomerase	e6yptD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
B	Pro_isomerase	e6yptB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
C	Pro_isomerase	e6yptC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
A	Beta-lactamase2	e6yptA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Beta-lactamase2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
A, C	PF05381	Tymovirus endopeptidase (Peptidase_C21)	Tymovirus endopeptidase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Polyubiquitin-C	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic 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 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
A, C	RNA replicase polyprotein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type endopeptidase activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA methyltransferase activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA methyltransferase activity RNA binding nucleic acid binding	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host ubiquitin-like protein modification symbiont-mediated perturbation of host process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction mRNA modification mRNA metabolic process RNA modification macromolecule modification methylation gene expression RNA processing proteolysis protein metabolic process DNA-templated transcription	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR019954	Ubiquitin conserved site	Conserved Site
B, D	IPR000626	Ubiquitin-like domain	Domain
B, D	IPR019956	Ubiquitin domain	Domain
B, D	IPR050158	Ubiquitin and ubiquitin-like	Family
B, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, C	IPR001788	RNA-dependent RNA polymerase, alsuviricetes	Domain
A, C	IPR043629	Salyut domain	Domain
A, C	IPR002588	Alphavirus-like methyltransferase domain	Domain
A, C	IPR027351	(+) RNA virus helicase core domain	Domain
A, C	IPR043181	Tymovirus endopeptidase domain	Homologous Superfamily
A, C	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR008043	Peptidase C21	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.