6ATK

Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth E]	SCOP2 Family	HCov-NL63 receptor-binding domain-like	8084628	4006418	SCOP2 (2022-06-29)
D [auth E]	SCOP2 Superfamily	SARS coronavirus receptor-binding domain-like	8084629	3001706	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	ERAP1 insert domain	8054110	3002272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Leukotriene A4 hydrolase N-terminal domain	8054108	3000390	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins) catalytic domain	8054109	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8054111	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ERAP1 insert domain	8054110	3002272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8054111	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins) catalytic domain	8054109	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Leukotriene A4 hydrolase N-terminal domain	8054108	3000390	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Leukotriene A4 hydrolase N-terminal domain	8054108	3000390	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8054111	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ERAP1 insert domain	8054110	3002272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metalloproteases (zincins) catalytic domain	8054109	3001975	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)
D [auth E]	PF01600	e6atkE1	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Alpha-coronavirus spike protein receptor-binding domain	F: PF01600	ECOD (1.6)
E [auth D]	PF01600	e6atkD1	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Alpha-coronavirus spike protein receptor-binding domain	F: PF01600	ECOD (1.6)
A	F_UNCLASSIFIED	e6atkA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF17900	e6atkA3	A: beta sandwiches	X: Baculovirus p35 protein-related (From Topology)	H: Baculovirus p35 protein-related (From Topology)	T: Baculovirus p35 protein-related	F: PF17900	ECOD (1.6)
A	PF11838	e6atkA4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF11838	ECOD (1.6)
A	PF01433	e6atkA1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: PF01433	ECOD (1.6)
B	F_UNCLASSIFIED	e6atkB4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF17900	e6atkB1	A: beta sandwiches	X: Baculovirus p35 protein-related (From Topology)	H: Baculovirus p35 protein-related (From Topology)	T: Baculovirus p35 protein-related	F: PF17900	ECOD (1.6)
B	PF11838	e6atkB2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF11838	ECOD (1.6)
B	PF01433	e6atkB3	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: PF01433	ECOD (1.6)
C	F_UNCLASSIFIED	e6atkC3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF17900	e6atkC4	A: beta sandwiches	X: Baculovirus p35 protein-related (From Topology)	H: Baculovirus p35 protein-related (From Topology)	T: Baculovirus p35 protein-related	F: PF17900	ECOD (1.6)
C	PF11838	e6atkC2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF11838	ECOD (1.6)
C	PF01433	e6atkC1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: PF01433	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	1.25.50.20	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth E], E [auth D], F	PF01600	Coronavirus spike glycoprotein S1 (CoV_S1)	Coronavirus spike glycoprotein S1	-	Family
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
D [auth E], E [auth D], F	Spike glycoprotein	-	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis import into cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell endocytosis transport of virus	membrane cellular anatomical entity virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part membrane cellular anatomical entity virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region viral membrane viral envelope
A, B, C	Aminopeptidase N	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity protein binding binding virus receptor activity exogenous protein binding molecular transducer activity signaling receptor activity aminopeptidase activity metalloaminopeptidase activity exopeptidase activity peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity protein binding binding virus receptor activity exogenous protein binding molecular transducer activity signaling receptor activity aminopeptidase activity metalloaminopeptidase activity exopeptidase activity metalloexopeptidase activity peptide binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular catabolic process organic substance metabolic process catabolic process cellular metabolic process metabolic process cellular process organic substance catabolic process peptide metabolic process peptide catabolic process developmental process cellular developmental process cell differentiation multicellular organismal process blood vessel morphogenesis cellular catabolic process organic substance metabolic process catabolic process cellular metabolic process metabolic process cellular process organic substance catabolic process peptide metabolic process peptide catabolic process developmental process cellular developmental process cell differentiation multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development organonitrogen compound metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle secretory granule secretory vesicle organelle membrane secretory granule membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome endoplasmic reticulum-Golgi intermediate compartment

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E], E [auth D], F	IPR002551	Spike glycoprotein S1, coronavirus	Domain
D [auth E], E [auth D], F	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
D [auth E], E [auth D], F	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
D [auth E], E [auth D], F	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
D [auth E], E [auth D], F	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
D [auth E], E [auth D], F	IPR042552	Spike glycoprotein, Alphacoronavirus	Family
D [auth E], E [auth D], F	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
D [auth E], E [auth D], F	IPR002552	Spike glycoprotein S2, coronavirus	Domain
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P15144	urinary bladder cancer pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis urinary bladder neoplasm ACUTE ALCOHOL WITHDRAWAL Barrett esophagus cancer ductal breast carcinoma in situ major depressive disorder malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia acute myeloid leukemia breast cancer Crohn disease urinary bladder cancer pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis urinary bladder neoplasm ACUTE ALCOHOL WITHDRAWAL Barrett esophagus cancer ductal breast carcinoma in situ major depressive disorder malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia acute myeloid leukemia breast cancer Crohn disease gallbladder disease malignant colon neoplasm nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma tuberculosis atypical teratoid rhabdoid tumor breast carcinoma cystic fibrosis lung carcinoma malignant mesothelioma non-small cell lung 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 R01GM133198.