6ATK | pdb_00006atk

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	Metalloproteases (zincins), catalytic domain	8054109	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Leukotriene A4 hydrolase N-terminal domain	8054108	3000390	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	Metalloproteases (zincins), catalytic domain	8054109	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8054111	3000116	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	ERAP1, insert domain	8054110	3002272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8054111	3000116	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]	RuBisCO_large_N	e6atkE1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: RuBisCO_large_N	ECOD (develop294)
E [auth D]	ATP-synt_Eps	e6atkD1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (develop294)
A	RuBisCO_large_N	e6atkA1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: RuBisCO_large_N	ECOD (develop294)
B	ATP-synt_Eps	e6atkB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (develop294)
C	ATP-synt_Eps	e6atkC1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (develop294)

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
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 symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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 cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part 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 alanyl aminopeptidase activity aminopeptidase 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 alanyl aminopeptidase activity aminopeptidase activity exopeptidase activity metalloaminopeptidase activity metalloexopeptidase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of systemic arterial blood pressure by renin-angiotensin regulation of systemic arterial blood pressure by hormone multicellular organismal process peptide hormone processing regulation of systemic arterial blood pressure mediated by a chemical signal system process signaling receptor ligand precursor processing protein maturation circulatory system process proteolysis protein metabolic process regulation of biological quality blood circulation regulation of blood pressure regulation of systemic arterial blood pressure by renin-angiotensin regulation of systemic arterial blood pressure by hormone multicellular organismal process peptide hormone processing regulation of systemic arterial blood pressure mediated by a chemical signal system process signaling receptor ligand precursor processing protein maturation circulatory system process proteolysis protein metabolic process regulation of biological quality blood circulation regulation of blood pressure regulation of hormone levels biological regulation regulation of systemic arterial blood pressure by circulatory renin-angiotensin primary metabolic process gene expression macromolecule biosynthetic process hormone metabolic process regulation of systemic arterial blood pressure endocrine process biosynthetic process regulation of angiotensin levels in blood protein processing metabolic process cellular process macromolecule metabolic process angiotensin maturation catabolic process peptide metabolic process peptide catabolic process developmental process cellular developmental process cell differentiation 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	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane 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 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 cytoplasm 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
A, B, C	IPR050344	Peptidase M1 family aminopeptidases	Family

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.