5KOV | pdb_00005kov

Crystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable fragment of an astrovirus neutralizing antibody at 3.24-A resolution

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth M]	SCOP2B Superfamily	Norovirus P2 domain-like	8093102	3002678	SCOP2B (2022-06-29)
P [auth T]	SCOP2B Superfamily	Norovirus P2 domain-like	8093102	3002678	SCOP2B (2022-06-29)
M [auth S]	SCOP2B Superfamily	Norovirus P2 domain-like	8093102	3002678	SCOP2B (2022-06-29)
I [auth N]	SCOP2B Superfamily	Norovirus P2 domain-like	8093102	3002678	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	Norovirus P2 domain-like	8093102	3002678	SCOP2B (2022-06-29)
E [auth H]	SCOP2B Superfamily	Norovirus P2 domain-like	8093102	3002678	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Norovirus P2 domain-like	8093102	3002678	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Norovirus P2 domain-like	8093102	3002678	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)
L [auth M]	PK_Tyr_Ser-Thr	e5kovM1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
P [auth T]	PK_Tyr_Ser-Thr	e5kovT1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
M [auth S]	PK_Tyr_Ser-Thr	e5kovS1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
I [auth N]	PK_Tyr_Ser-Thr	e5kovN1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
H [auth G]	PK_Tyr_Ser-Thr	e5kovG1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
E [auth H]	PK_Tyr_Ser-Thr	e5kovH1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
D [auth B]	PK_Tyr_Ser-Thr	e5kovB1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
A	PK_Tyr_Ser-Thr	e5kovA1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
O [auth U]	PK_Tyr_Ser-Thr	e5kovU1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
N [auth W]	Aldedh	e5kovW1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Aldedh	ECOD (v294.1)
K [auth O]	PK_Tyr_Ser-Thr	e5kovO1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
J [auth Q]	SelB-wing_3	e5kovQ1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: SelB-wing_3	ECOD (v294.1)
G [auth I]	PK_Tyr_Ser-Thr	e5kovI1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
F [auth K]	PK_Tyr_Ser-Thr	e5kovK1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
C [auth E]	PK_Tyr_Ser-Thr	e5kovE1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
B [auth C]	PK_Tyr_Ser-Thr	e5kovC1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: PK_Tyr_Ser-Thr	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
O [auth U]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [auth O]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B], E [auth H], H [auth G], I [auth N], A, D [auth B], E [auth H], H [auth G], I [auth N], L [auth M], M [auth S], P [auth T]	Capsid polyprotein VP90	-	import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component host cellular component host extracellular region cellular anatomical structure other organism part
B [auth C], C [auth E], F [auth K], G [auth I], J [auth Q], B [auth C], C [auth E], F [auth K], G [auth I], J [auth Q], K [auth O], N [auth W], O [auth U]	PL-2 scFv chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B], E [auth H], H [auth G], I [auth N], A, D [auth B], E [auth H], H [auth G], I [auth N], L [auth M], M [auth S], P [auth T]	IPR004337	Astrovirus capsid protein, inner core domain	Domain
A, D [auth B], E [auth H], H [auth G], I [auth N], A, D [auth B], E [auth H], H [auth G], I [auth N], L [auth M], M [auth S], P [auth T]	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, D [auth B], E [auth H], H [auth G], I [auth N], A, D [auth B], E [auth H], H [auth G], I [auth N], L [auth M], M [auth S], P [auth T]	IPR022027	Turkey astrovirus capsid protein	Family

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.