1X3Z | pdb_00001x3z

Structure of a peptide:N-glycanase-Rad23 complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1x3zb_	All alpha proteins	XPC-binding domain-like	XPC-binding domain	XPC-binding domain	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1x3za_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Transglutaminase core	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	XPC-binding domain	8021209	4000673	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	XPC-binding domain	8033589	3000974	SCOP2 (2022-06-29)
A	SCOP2 Family	Transglutaminase core	8021207	4000877	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cysteine proteinases	8033587	3001808	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	XPC-binding	e1x3zB1	A: alpha arrays	X: HTH	H: XPC-binding domain (From Topology)	T: XPC-binding domain	F: XPC-binding	ECOD (1.6)
A	Transglut_core	e1x3zA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Transglut_core	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.10.540	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	XPC-binding domain	CATH (4.3.0)
A	6.10.250.270	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.10.1740.90	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)
A	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	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
A	PF01841	Transglutaminase-like superfamily (Transglut_core)	Transglutaminase-like superfamily	This domain is found in animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that ...	This domain is found in animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' [1]. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase [2], it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease. [3]	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth I]	peptide PHQ-Val-Ala-Asp-CF0	-	-	-
B	UV excision repair protein RAD23	polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin binding ubiquitin-like protein binding protein-containing complex binding proteasome binding DNA binding damaged DNA binding nucleic acid binding protein-macromolecule adaptor activity molecular adaptor activity	cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress nucleotide-excision repair, DNA damage recognition chromosome organization DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing 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 RNA metabolic process 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 biosynthetic 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 negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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
A	peptide: N-glycanase	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process carbohydrate derivative metabolic process ubiquitin-dependent glycoprotein ERAD pathway macromolecule catabolic process response to glycoprotein ERAD pathway cellular response to stress response to stress proteolysis protein metabolic process response to endoplasmic reticulum stress cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process carbohydrate derivative metabolic process ubiquitin-dependent glycoprotein ERAD pathway macromolecule catabolic process response to glycoprotein ERAD pathway cellular response to stress response to stress proteolysis protein metabolic process response to endoplasmic reticulum stress carbohydrate derivative catabolic process glycoprotein catabolic process response to oxygen-containing compound primary metabolic process response to nitrogen compound proteasomal protein catabolic process protein catabolic process glycoprotein metabolic process response to chemical metabolic process cellular process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex peptidase complex PNGase complex cytosol nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR004806	UV excision repair protein Rad23	Family
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR036353	XPC-binding domain superfamily	Homologous Superfamily
B	IPR015360	XPC-binding domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR009060	UBA-like superfamily	Homologous Superfamily
B	IPR015940	Ubiquitin-associated domain	Domain
B	IPR006636	Heat shock chaperonin-binding	Domain
A	IPR050883	Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase	Family
A	IPR002931	Transglutaminase-like	Domain
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily

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.