4S1Z

Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4s1za_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4s1zb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4s1zc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4s1zd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4s1ze_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	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	8066187	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
F	SCOP2 Family	Ran binding protein zinc finger-like	8081674	4000343	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Ran binding protein zinc finger-like	8081675	3000133	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Ran binding protein zinc finger-like	8081675	3000133	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ran binding protein zinc finger-like	8081675	3000133	SCOP2B (2022-06-29)
I [auth J]	SCOP2B Superfamily	Ran binding protein zinc finger-like	8081675	3000133	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	Ran binding protein zinc finger-like	8081675	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	e4s1zA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	ubiquitin_1	e4s1zB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
C	ubiquitin_1	e4s1zC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D	ubiquitin_1	e4s1zD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
E	ubiquitin_1	e4s1zE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
F	zf-RanBP	e4s1zF1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
G	zf-RanBP	e4s1zG1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
H	zf-RanBP	e4s1zH1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
I [auth J]	zf-RanBP	e4s1zJ1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
J [auth I]	zf-RanBP	e4s1zI1	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Ubiquitin	structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification 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 macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification 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 protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal biosynthetic process cytoplasmic translation translation gene expression macromolecule biosynthetic process	membrane-bounded organelle cellular anatomical structure organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery membrane-bounded organelle cellular anatomical structure organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome cytosolic ribosome membraneless organelle intracellular membraneless organelle ribosome endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit
F, G, H, I [auth J], J [auth I]	Ubiquitin thioesterase ZRANB1	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 primary metabolic process protein catabolic process protein deubiquitination involved in ubiquitin-dependent protein catabolic process macromolecule catabolic process protein modification by small protein removal modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis macromolecule modification metabolic process cellular process protein deubiquitination catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process protein deubiquitination involved in ubiquitin-dependent protein catabolic process macromolecule catabolic process protein modification by small protein removal modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis macromolecule modification metabolic process cellular process ubiquitin-dependent protein catabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal cellular component organization organelle organization 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	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

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	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
A, B, C, D, E	IPR050158	Ubiquitin and ubiquitin-like	Family
A, B, C, D, E	IPR000626	Ubiquitin-like domain	Domain
A, B, C, D, E	IPR019956	Ubiquitin domain	Domain
A, B, C, D, E	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
A, B, C, D, E	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
F, G, H, I [auth J], J [auth I]	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
F, G, H, I [auth J], J [auth I]	IPR051346	OTU Domain-Containing Deubiquitinase	Family
F, G, H, I [auth J], J [auth I]	IPR049768	Ubiquitin thioesterase ZRANB1, ovarian tumor domain	Domain
F, G, H, I [auth J], J [auth I]	IPR041294	Ankyrin ubiquitin-binding domain	Domain
F, G, H, I [auth J], J [auth I]	IPR003323	OTU domain	Domain
F, G, H, I [auth J], J [auth I]	IPR001876	Zinc finger, RanBP2-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	Pharos: P62987	attention deficit hyperactivity disorder, inattentive type heart disease dental caries lung cancer gastroesophageal reflux disease plasma cell myeloma

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.