Annotations: 2QSF

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	beta-hairpin DNA-binding domain-like	8052784	3002139	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-hairpin DNA-binding domain-like	8052785	3002139	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8052789	3001808	SCOP2B (2022-06-29)
B [auth X]	SCOP2B Superfamily	XPC-binding domain	8033589	3000974	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	PF10405	e2qsfA6	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: PF10405	ECOD (1.6)
A	F_UNCLASSIFIED	e2qsfA5	A: alpha arrays	X: DNA repair protein RAD4 beta-hairpin domain (From Topology)	H: DNA repair protein RAD4 beta-hairpin domain (From Topology)	T: DNA repair protein RAD4 beta-hairpin domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF10403	e2qsfA3	A: alpha arrays	X: DNA repair protein RAD4 beta-hairpin domain (From Topology)	H: DNA repair protein RAD4 beta-hairpin domain (From Topology)	T: DNA repair protein RAD4 beta-hairpin domain	F: PF10403	ECOD (1.6)
A	PF03835	e2qsfA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF03835	ECOD (1.6)
B [auth X]	PF09280	e2qsfX1	A: alpha arrays	X: HTH	H: XPC-binding domain (From Topology)	T: XPC-binding domain	F: PF09280	ECOD (1.6)
B [auth X]	PF00627	e2qsfX2	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: PF00627	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.260.10	Alpha Beta	Alpha-Beta Complex	Coagulation Factor XIII	Chain A, domain 2	CATH (4.3.0)
A	2.20.20.110	Mainly Beta	Single Sheet	Anthopleurin-A	Rad4, beta-hairpin domain BHD1	CATH (4.3.0)
A	3.30.60.290	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	3.30.70.2460	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Rad4, beta-hairpin domain BHD3	CATH (4.3.0)
B [auth X]	1.10.10.540	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	XPC-binding domain	CATH (4.3.0)
B [auth X]	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03835	Rad4 transglutaminase-like domain (Rad4)	Rad4 transglutaminase-like domain	-	Domain
A	PF10405	Rad4 beta-hairpin domain 3 (BHD_3)	Rad4 beta-hairpin domain 3	This short domain is found in the Rad4 protein. This domain binds to DNA [1].	Domain
A	PF10403	Rad4 beta-hairpin domain 1 (BHD_1)	Rad4 beta-hairpin domain 1	This short domain is found in the Rad4 protein. This domain binds to DNA [1].	Domain
B [auth X]	PF00627	UBA/TS-N domain (UBA)	UBA/TS-N domain	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin a ...	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle [1]. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU [2]. The domain has been found in non EF-TS proteins such as alpha-NAC Swiss:P70670 and MJ0280 Swiss:Q57728 [1].	Domain
B [auth X]	PF09280	XPC-binding domain (XPC-binding)	XPC-binding domain	Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA repair protein RAD4	DNA binding binding organic cyclic compound binding damaged DNA binding single-strand break-containing DNA binding nucleic acid binding single-stranded DNA binding	cellular response to stimulus mismatch repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process cellular response to stimulus mismatch repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair nucleotide-excision repair, DNA damage recognition chromosome organization cellular component organization organelle organization nucleotide-excision repair cellular component organization or biogenesis regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process negative regulation of biosynthetic process DNA conformation change DNA topological change organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein metabolic process organic substance catabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity nucleotide-excision repair factor 2 complex intracellular organelle organelle nucleotide-excision repair complex cytoplasm cytosol XPC complex
B [auth X]	UV excision repair protein RAD23	protein binding binding ubiquitin binding ubiquitin-like protein binding DNA binding organic cyclic compound binding damaged DNA binding nucleic acid binding protein-macromolecule adaptor activity molecular adaptor activity polyubiquitin modification-dependent protein binding modification-dependent protein binding protein-containing complex binding proteasome binding	organonitrogen compound metabolic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process organic substance metabolic process macromolecule modification protein deglycosylation metabolic process protein metabolic process macromolecule metabolic process protein modification process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process organonitrogen compound metabolic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process organic substance metabolic process macromolecule modification protein deglycosylation metabolic process protein metabolic process macromolecule metabolic process protein modification process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process organic substance catabolic process cellular response to stimulus response to organic substance response to stimulus ubiquitin-dependent glycoprotein ERAD pathway response to glycoprotein ERAD pathway cellular response to stress response to stress response to endoplasmic reticulum stress carbohydrate derivative catabolic process glycoprotein catabolic process response to organonitrogen compound response to oxygen-containing compound response to nitrogen compound response to chemical cellular process nucleotide-excision repair, DNA damage recognition chromosome organization DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process organic cyclic compound metabolic process organelle organization nucleotide-excision repair DNA damage response cellular component organization or biogenesis DNA repair regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process negative regulation of biosynthetic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex nucleotide-excision repair factor 2 complex nucleotide-excision repair complex catalytic complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex nucleotide-excision repair factor 2 complex nucleotide-excision repair complex catalytic complex peptidase complex PNGase complex cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018326	Rad4 beta-hairpin domain 1	Domain
A	IPR042488	Rad4, beta-hairpin domain 3 superfamily	Homologous Superfamily
A	IPR036985	Transglutaminase-like superfamily	Homologous Superfamily
A	IPR018325	Rad4/PNGase transglutaminase-like fold	Domain
A	IPR004583	DNA repair protein Rad4	Family
A	IPR018328	Rad4 beta-hairpin domain 3	Domain
A	IPR018026	DNA repair protein Rad4-like	Family
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR018327	Rad4 beta-hairpin domain 2	Domain
B [auth X]	IPR004806	UV excision repair protein Rad23	Family
B [auth X]	IPR036353	XPC-binding domain superfamily	Homologous Superfamily
B [auth X]	IPR015360	XPC-binding domain	Domain
B [auth X]	IPR015940	Ubiquitin-associated domain	Domain
B [auth X]	IPR000626	Ubiquitin-like domain	Domain
B [auth X]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth X]	IPR009060	UBA-like superfamily	Homologous Superfamily
B [auth X]	IPR006636	Heat shock chaperonin-binding	Domain

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 R01GM133198.