5XIT | pdb_00005xit

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II

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 [auth D]	d5xitd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d5xitf_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth H]	d5xith_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth B]	d5xitb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2 Family	Ubiquitin-related	8098881	4000962	SCOP2 (2022-06-29)
A [auth D]	SCOP2 Superfamily	Ubiquitin-like	8098882	3000157	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8098882	3000157	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	Ubiquitin-like	8098882	3000157	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Ubiquitin-like	8098882	3000157	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 [auth D]	Ig_2	e5xitD1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Ig_2	ECOD (develop294)
F	Ig_2	e5xitF1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Ig_2	ECOD (develop294)
C [auth H]	Ig_2	e5xitH1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Ig_2	ECOD (develop294)
E [auth B]	Ig_2	e5xitB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Ig_2	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], F	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
C [auth H], E [auth B]	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 [auth D], F	Ubiquitin-40S ribosomal protein S27a	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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding 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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	translation at synapse primary metabolic process translation at presynapse translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process catabolic process modification-dependent macromolecule catabolic process translation at synapse primary metabolic process translation at presynapse translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process protein catabolic 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 cytoplasmic translation cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis ribosomal small subunit biogenesis translation at postsynapse	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen myelin sheath cytoplasm cytosol presynapse synapse cell junction nucleoplasm ribosome cytosolic ribosome protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex cytosolic small ribosomal subunit small ribosomal subunit ribosomal subunit postsynapse endoplasmic reticulum endomembrane system
B [auth E], D [auth A]	E3 ubiquitin-protein ligase RNF168	protein binding binding histone binding aminoacyltransferase activity histone H2A ubiquitin ligase activity catalytic activity, acting on a protein acyltransferase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity histone H2AK15 ubiquitin ligase activity ubiquitin-like protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity protein binding binding histone binding aminoacyltransferase activity histone H2A ubiquitin ligase activity catalytic activity, acting on a protein acyltransferase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity histone H2AK15 ubiquitin ligase activity ubiquitin-like protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity histone modifying activity catalytic activity chromatin binding ubiquitin binding ubiquitin-like protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding protein-containing complex binding nucleosome binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA repair-dependent chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis double-strand break repair via classical nonhomologous end joining double-strand break repair double-strand break repair via nonhomologous end joining cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA repair-dependent chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis double-strand break repair via classical nonhomologous end joining double-strand break repair double-strand break repair via nonhomologous end joining primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process transcription elongation by RNA polymerase II negative regulation of biological process RNA metabolic process negative regulation of transcription elongation by RNA polymerase II regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of DNA-templated transcription elongation negative regulation of DNA-templated transcription regulation of transcription elongation by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process negative regulation of DNA-templated transcription, elongation DNA-templated transcription elongation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process interstrand cross-link repair protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of biological process regulation of cellular response to stress positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus regulation of DNA metabolic process catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process response to ionizing radiation response to radiation response to abiotic stimulus protein polyubiquitination protein K63-linked ubiquitination immune system development adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process lymphocyte mediated immunity immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination B cell activation involved in immune response lymphocyte activation cell activation involved in immune response leukocyte activation multicellular organism development somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response anatomical structure development leukocyte mediated immunity somatic diversification of immune receptors lymphocyte activation involved in immune response somatic recombination of immunoglobulin genes involved in immune response system development developmental process production of molecular mediator of immune response immune response B cell activation DNA recombination cell activation immunoglobulin mediated immune response adaptive immune response immune effector process somatic diversification of immunoglobulins immune system process somatic diversification of immune receptors via germline recombination within a single locus B cell mediated immunity isotype switching	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex
C [auth H], E [auth B]	Ubiquitin-40S ribosomal protein S27a	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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding 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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	translation at synapse primary metabolic process translation at presynapse translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process catabolic process modification-dependent macromolecule catabolic process translation at synapse primary metabolic process translation at presynapse translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process protein catabolic 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 cytoplasmic translation cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis ribosomal small subunit biogenesis translation at postsynapse	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen myelin sheath cytoplasm cytosol presynapse synapse cell junction nucleoplasm ribosome cytosolic ribosome protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex cytosolic small ribosomal subunit small ribosomal subunit ribosomal subunit postsynapse endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], F	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth D], F	IPR038582	Small ribosomal subunit protein eS31 eukaryotic superfamily	Homologous Superfamily
A [auth D], F	IPR050158	Ubiquitin and ubiquitin-like	Family
A [auth D], F	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
A [auth D], F	IPR000626	Ubiquitin-like domain	Domain
A [auth D], F	IPR002906	Small ribosomal subunit protein eS31	Domain
A [auth D], F	IPR019956	Ubiquitin domain	Domain
A [auth D], F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth E], D [auth A]	IPR051657	RNF168/RNF169 E3 ubiquitin-protein ligase	Family
B [auth E], D [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth E], D [auth A]	IPR034725	E3 ubiquitin-protein ligase RNF168	Family
B [auth E], D [auth A]	IPR001841	Zinc finger, RING-type	Domain
C [auth H], E [auth B]	IPR019954	Ubiquitin conserved site	Conserved Site
C [auth H], E [auth B]	IPR038582	Small ribosomal subunit protein eS31 eukaryotic superfamily	Homologous Superfamily
C [auth H], E [auth B]	IPR050158	Ubiquitin and ubiquitin-like	Family
C [auth H], E [auth B]	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
C [auth H], E [auth B]	IPR000626	Ubiquitin-like domain	Domain
C [auth H], E [auth B]	IPR002906	Small ribosomal subunit protein eS31	Domain
C [auth H], E [auth B]	IPR019956	Ubiquitin domain	Domain
C [auth H], E [auth B]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth E], D [auth A]	Pharos: Q8IYW5	RIDDLE syndrome hereditary spastic paraplegia ovarian cancer intellectual disability osteosarcoma

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.

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