5AF6

Structure of Lys33-linked diUb bound to Trabid NZF1

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)
A	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
G	SCOP2 Family	Ran binding protein zinc finger-like	8081672	4000343	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Ran binding protein zinc finger-like	8081673	3000133	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	Ran binding protein zinc finger-like	8081673	3000133	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ran binding protein zinc finger-like	8081673	3000133	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ran binding protein zinc finger-like	8081673	3000133	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ran binding protein zinc finger-like	8081673	3000133	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	e5af6A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
C	ubiquitin_1	e5af6C1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	ubiquitin_1	e5af6B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D	ubiquitin_1	e5af6D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
E	ubiquitin_1	e5af6E1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
G	zf-RanBP	e5af6G1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
I	zf-RanBP	e5af6I1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
F	zf-RanBP	e5af6F1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
H	zf-RanBP	e5af6H1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
J	zf-RanBP	e5af6J1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	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
F, G, H, I, J	PF00641	Zn-finger in Ran binding protein and others (zf-RanBP)	Zn-finger in Ran binding protein and others	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	UBIQUITIN	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis nitrogen compound metabolic process metabolic process protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis nitrogen compound metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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
F, G, H, I, J	TRABID	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 polyubiquitin modification-dependent protein binding protein binding binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding cation 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 polyubiquitin modification-dependent protein binding protein binding binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding cation binding ion binding metal ion binding small molecule binding	protein deubiquitination catabolic process proteolysis involved in protein catabolic process macromolecule catabolic process organic substance metabolic process protein modification by small protein removal modification-dependent macromolecule catabolic process proteolysis nitrogen compound metabolic process protein metabolic process protein modification process organonitrogen compound catabolic process organonitrogen compound metabolic process primary metabolic process protein deubiquitination catabolic process proteolysis involved in protein catabolic process macromolecule catabolic process organic substance metabolic process protein modification by small protein removal modification-dependent macromolecule catabolic process proteolysis nitrogen compound metabolic process protein metabolic process protein modification process organonitrogen compound catabolic process organonitrogen compound metabolic process primary metabolic process protein catabolic process protein deubiquitination involved in ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process macromolecule modification metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process post-translational protein modification organic substance catabolic process protein modification by small protein conjugation or removal cellular component organization organelle organization cellular process cellular component organization or biogenesis cytoskeleton organization cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway biological regulation regulation of response to stimulus regulation of cell communication positive regulation of signaling protein K29-linked deubiquitination developmental process anatomical structure morphogenesis regulation of developmental process anatomical structure development cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis protein K33-linked deubiquitination cell migration cell motility protein K63-linked deubiquitination	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR019954	Ubiquitin conserved site	Conserved Site
A, B, C, D, E	IPR000626	Ubiquitin-like domain	Domain
A, B, C, D, E	IPR019956	Ubiquitin domain	Domain
A, B, C, D, E	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
F, G, H, I, J	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
F, G, H, I, J	IPR049768	Ubiquitin thioesterase ZRANB1, ovarian tumor domain	Domain
F, G, H, I, J	IPR041294	Ankyrin ubiquitin-binding domain	Domain
F, G, H, I, J	IPR003323	OTU domain	Domain
F, G, H, I, J	IPR001876	Zinc finger, RanBP2-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	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
F, G, H, I, J	Pharos: Q9UGI0	acute myeloid leukemia glioblastoma osteosarcoma prostate carcinoma adrenal cortex carcinoma large cell medulloblastoma ovarian cancer spina bifida atypical teratoid rhabdoid tumor malignant glioma pancreatic ductal adenocarcinoma subependymal giant cell astrocytoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.