3QNF | pdb_00003qnf

Crystal structure of the open state of human endoplasmic reticulum aminopeptidase 1 ERAP1

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d3qnfc4	All alpha proteins	alpha-alpha superhelix	ARM repeat	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3qnfc3	All beta proteins	Immunoglobulin-like beta-sandwich	Zn aminopeptidase insert domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3qnfc1	All beta proteins	Zn aminopeptidase N-terminal domain	Zn aminopeptidase N-terminal domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3qnfc2	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qnfb4	All alpha proteins	alpha-alpha superhelix	ARM repeat	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qnfb3	All beta proteins	Immunoglobulin-like beta-sandwich	Zn aminopeptidase insert domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qnfb1	All beta proteins	Zn aminopeptidase N-terminal domain	Zn aminopeptidase N-terminal domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qnfb2	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qnfa3	All beta proteins	Immunoglobulin-like beta-sandwich	Zn aminopeptidase insert domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qnfa1	All beta proteins	Zn aminopeptidase N-terminal domain	Zn aminopeptidase N-terminal domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qnfa2	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	automated matches	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)
C	SCOP2B Superfamily	ARM repeat-like	8054063	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8054062	3001975	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ERAP1, insert domain	8054058	3002272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Leukotriene A4 hydrolase N-terminal domain	8054061	3000390	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8054063	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Leukotriene A4 hydrolase N-terminal domain	8054061	3000390	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ERAP1, insert domain	8054058	3002272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8054062	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8054062	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Leukotriene A4 hydrolase N-terminal domain	8054061	3000390	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ERAP1, insert domain	8054058	3002272	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)
C	Plexin_RBD	e3qnfC1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Plexin_RBD	ECOD (v294.1)
C	ERAP1_C	e3qnfC3	A: a/b three-layered sandwiches	X: ACP-like	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: ERAP1_C	ECOD (v294.1)
B	CBM32	e3qnfB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: CBM32	ECOD (v294.1)
B	ERAP1_C	e3qnfB2	A: a/b three-layered sandwiches	X: ACP-like	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: ERAP1_C	ECOD (v294.1)
A	Aldedh	e3qnfA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Aldedh	ECOD (v294.1)
A	Peptidase_S26	e3qnfA4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.1730	Mainly Beta	Sandwich	Immunoglobulin-like	tricorn interacting facor f3 domain	CATH (4.3.0)
C	1.10.390.10	Mainly Alpha	Orthogonal Bundle	Neutral Protease	domain 2	CATH (4.3.0)
C	2.60.40.1910	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	1.25.50.20	Mainly Alpha	Alpha Horseshoe	Zincin-like fold		CATH (4.3.0)
B	2.60.40.1730	Mainly Beta	Sandwich	Immunoglobulin-like	tricorn interacting facor f3 domain	CATH (4.3.0)
B	1.10.390.10	Mainly Alpha	Orthogonal Bundle	Neutral Protease	domain 2	CATH (4.3.0)
B	2.60.40.1910	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	1.25.50.20	Mainly Alpha	Alpha Horseshoe	Zincin-like fold		CATH (4.3.0)
A	2.60.40.1730	Mainly Beta	Sandwich	Immunoglobulin-like	tricorn interacting facor f3 domain	CATH (4.3.0)
A	1.10.390.10	Mainly Alpha	Orthogonal Bundle	Neutral Protease	domain 2	CATH (4.3.0)
A	2.60.40.1910	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	1.10.3480.20	Mainly Alpha	Orthogonal Bundle	TorD-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF11838	ERAP1-like C-terminal domain (ERAP1_C)	ERAP1-like C-terminal domain	This large domain is composed of 16 alpha helices organized as 8 HEAT-like repeats. This domain forms a concave face that faces towards the active site of the peptidase.	Domain
A, B, C	PF01433	Peptidase family M1 domain (Peptidase_M1)	Peptidase family M1 domain	Members of this family are aminopeptidases. The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues. This family includes leukotriene-A4 hydrolase Swiss:P09960, this enzyme also has an aminopeptidase activ ...	Members of this family are aminopeptidases. The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues. This family includes leukotriene-A4 hydrolase Swiss:P09960, this enzyme also has an aminopeptidase activity [1].	Domain
A, B, C	PF17900	Peptidase M1 N-terminal domain (Peptidase_M1_N)	Peptidase M1 N-terminal domain	This domain is found at the N-terminus of aminopeptidases from the M1 family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Endoplasmic reticulum aminopeptidase 1	interleukin-1, type II receptor binding protein binding binding interleukin-1 receptor binding signaling receptor binding cytokine receptor binding growth factor receptor binding peptidase activity catalytic activity, acting on a protein hydrolase activity metallopeptidase activity aminopeptidase activity metalloaminopeptidase activity exopeptidase activity interleukin-1, type II receptor binding protein binding binding interleukin-1 receptor binding signaling receptor binding cytokine receptor binding growth factor receptor binding peptidase activity catalytic activity, acting on a protein hydrolase activity metallopeptidase activity aminopeptidase activity metalloaminopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity interleukin-6 receptor binding endopeptidase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	catabolic process metabolic process cellular process peptide metabolic process peptide catabolic process multicellular organismal process system process circulatory system process regulation of blood pressure biological regulation regulation of biological quality blood circulation response to stimulus immune response catabolic process metabolic process cellular process peptide metabolic process peptide catabolic process multicellular organismal process system process circulatory system process regulation of blood pressure biological regulation regulation of biological quality blood circulation response to stimulus immune response immune system process adaptive immune response developmental process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus response to biotic stimulus response to stress regulation of response to stress innate immune response regulation of immune system process response to external biotic stimulus regulation of biological process response to other organism defense response regulation of innate immune response defense response to symbiont response to external stimulus regulation of response to stimulus defense response to other organism regulation of immune response regulation of developmental process positive regulation of biological process regulation of vasculature development positive regulation of developmental process regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process response to bacterium fat cell differentiation cellular developmental process cell differentiation antigen processing and presentation antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I proteolysis primary metabolic process protein metabolic process macromolecule metabolic process membrane protein proteolysis membrane protein ectodomain proteolysis	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001930	Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase	Family
A, B, C	IPR042097	Aminopeptidase N-like , N-terminal domain superfamliy	Homologous Superfamily
A, B, C	IPR024571	ERAP1-like C-terminal domain	Domain
A, B, C	IPR027268	Peptidase M4/M1, CTD superfamily	Homologous Superfamily
A, B, C	IPR034016	Aminopeptidase N-type	Family
A, B, C	IPR014782	Peptidase M1, membrane alanine aminopeptidase	Domain
A, B, C	IPR045357	Aminopeptidase N-like , N-terminal domain	Domain
A, B, C	IPR050344	Peptidase M1 family aminopeptidases	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q9NZ08	ankylosing spondylitis psoriasis hypertensive disorder Behcet disease Crohn disease Liver Cirrhosis, Experimental lung cancer malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm Sjogren syndrome attention deficit hyperactivity disorder, inattentive type breast cancer ductal breast carcinoma in situ juvenile idiopathic arthritis malignant ependymoma ankylosing spondylitis psoriasis hypertensive disorder Behcet disease Crohn disease Liver Cirrhosis, Experimental lung cancer malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm Sjogren syndrome attention deficit hyperactivity disorder, inattentive type breast cancer ductal breast carcinoma in situ juvenile idiopathic arthritis malignant ependymoma osteosarcoma pilocytic astrocytoma anterior uveitis tuberculosis atypical teratoid rhabdoid tumor breast carcinoma cystic fibrosis esophageal adenocarcinoma inflammatory bowel disease malignant glioma ovarian cancer plasma cell myeloma pustulosis palmaris et plantaris astrocytic tumor ulcerative colitis common variable immunodeficiency diabetes mellitus glioblastoma invasive ductal breast carcinoma

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.