Annotations: 1CD3

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth 1]	d1cd31_	All alpha proteins	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	(Sinsheimervirus phiX174 ) [TaxId: 10847 ],	SCOPe (2.08)
B [auth 2]	d1cd32_	All alpha proteins	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	(Sinsheimervirus phiX174 ) [TaxId: 10847 ],	SCOPe (2.08)
C [auth 3]	d1cd33_	All alpha proteins	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	(Sinsheimervirus phiX174 ) [TaxId: 10847 ],	SCOPe (2.08)
D [auth 4]	d1cd34_	All alpha proteins	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	Scaffolding protein gpD of bacteriophage procapsid	(Sinsheimervirus phiX174 ) [TaxId: 10847 ],	SCOPe (2.08)
E [auth F]	d1cd3f_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	ssDNA viruses	Microviridae-like VP	Microvirus capsid proteins, capsid protein F	(Sinsheimervirus phiX174 ) [TaxId: 10847 ],	SCOPe (2.08)
F [auth G]	d1cd3g_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	ssDNA viruses	Microviridae-like VP	Microvirus capsid proteins, spike protein G	(Sinsheimervirus phiX174 ) [TaxId: 10847 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth 1]	SCOP2B Superfamily	Scaffolding protein gpD of bacteriophage procapsid	8032652	3000749	SCOP2B (2022-06-29)
B [auth 2]	SCOP2B Superfamily	Scaffolding protein gpD of bacteriophage procapsid	8032652	3000749	SCOP2B (2022-06-29)
C [auth 3]	SCOP2B Superfamily	Scaffolding protein gpD of bacteriophage procapsid	8032652	3000749	SCOP2B (2022-06-29)
D [auth 4]	SCOP2B Superfamily	Scaffolding protein gpD of bacteriophage procapsid	8032652	3000749	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	ssDNA viruses	8040766	3000931	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)
A [auth 1]	gpD	e1cd311	A: alpha arrays	X: Scaffolding protein gpD of bacteriophage procapsid (From Topology)	H: Scaffolding protein gpD of bacteriophage procapsid (From Topology)	T: Scaffolding protein gpD of bacteriophage procapsid	F: gpD	ECOD (1.6)
B [auth 2]	gpD	e1cd321	A: alpha arrays	X: Scaffolding protein gpD of bacteriophage procapsid (From Topology)	H: Scaffolding protein gpD of bacteriophage procapsid (From Topology)	T: Scaffolding protein gpD of bacteriophage procapsid	F: gpD	ECOD (1.6)
C [auth 3]	gpD	e1cd331	A: alpha arrays	X: Scaffolding protein gpD of bacteriophage procapsid (From Topology)	H: Scaffolding protein gpD of bacteriophage procapsid (From Topology)	T: Scaffolding protein gpD of bacteriophage procapsid	F: gpD	ECOD (1.6)
D [auth 4]	gpD	e1cd342	A: alpha arrays	X: Scaffolding protein gpD of bacteriophage procapsid (From Topology)	H: Scaffolding protein gpD of bacteriophage procapsid (From Topology)	T: Scaffolding protein gpD of bacteriophage procapsid	F: gpD	ECOD (1.6)
E [auth F]	Phage_F	e1cd3F1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Phage_F	ECOD (1.6)
F [auth G]	Phage_G	e1cd3G1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Phage_G	ECOD (1.6)
G [auth B]	Phage_B	e1cd3B1	A: a+b complex topology	X: Scaffolding protein GPB (From Topology)	H: Scaffolding protein GPB (From Topology)	T: Scaffolding protein GPB	F: Phage_B	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth 1]	1.10.1850.10	Mainly Alpha	Orthogonal Bundle	Procapsid Of Bacteriophage Phix174, Chain 1	Scaffold protein D	CATH (4.3.0)
B [auth 2]	1.10.1850.10	Mainly Alpha	Orthogonal Bundle	Procapsid Of Bacteriophage Phix174, Chain 1	Scaffold protein D	CATH (4.3.0)
C [auth 3]	1.10.1850.10	Mainly Alpha	Orthogonal Bundle	Procapsid Of Bacteriophage Phix174, Chain 1	Scaffold protein D	CATH (4.3.0)
D [auth 4]	1.10.1850.10	Mainly Alpha	Orthogonal Bundle	Procapsid Of Bacteriophage Phix174, Chain 1	Scaffold protein D	CATH (4.3.0)
E [auth F]	2.60.169.10	Mainly Beta	Sandwich	Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1	Microviridae F protein	CATH (4.3.0)
F [auth G]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
G [auth B]	4.10.1260.10	Few Secondary Structures	Irregular	Scaffolding protein gpD of bacteriophage procapsid fold	Scaffolding protein gpD of bacteriophage procapsid	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 1], B [auth 2], C [auth 3], D [auth 4]	PF02925	Bacteriophage scaffolding protein D (gpD)	Bacteriophage scaffolding protein D	-	Domain
E [auth F]	PF02305	Capsid protein (F protein) (Phage_F)	Capsid protein (F protein)	This is a family of proteins from single-stranded DNA bacteriophages. Protein F is the major capsid component, sixty copies of which are found in the virion.	Domain
F [auth G]	PF02306	Major spike protein (G protein) (Phage_G)	Major spike protein (G protein)	This is a family of proteins from single-stranded DNA bacteriophages. Five G proteins, each a tight beta barrel, from twelve surface spikes.	Domain
G [auth B]	PF02304	Scaffold protein B (Phage_B)	Scaffold protein B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 1], B [auth 2], C [auth 3], D [auth 4]	PROTEIN (SCAFFOLDING PROTEIN GPD)	-	virus maturation viral life cycle viral capsid assembly viral procapsid maturation cellular component biogenesis cellular component organization virion assembly cellular component assembly viral process cellular process cellular component organization or biogenesis	host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity
E [auth F]	PROTEIN (CAPSID PROTEIN GPF)	structural molecule activity	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction	viral capsid icosahedral viral capsid virion component T=1 icosahedral viral capsid
F [auth G]	PROTEIN (SPIKE PROTEIN GPG)	-	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host modulation by symbiont of host process modulation by virus of host process modulation of process of another organism	viral capsid virion component host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity
G [auth B]	PROTEIN (SCAFFOLDING PROTEIN GPB)	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity	virion assembly viral process viral scaffold assembly and maintenance viral capsid assembly viral life cycle organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	protein-containing complex viral capsid virion component viral scaffold host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 1], B [auth 2], C [auth 3], D [auth 4]	IPR036632	Scaffold protein D superfamily	Homologous Superfamily
A [auth 1], B [auth 2], C [auth 3], D [auth 4]	IPR004196	Scaffold protein D	Family
E [auth F]	IPR016184	Capsid/spike protein, ssDNA virus	Homologous Superfamily
E [auth F]	IPR003514	Microviridae F protein	Family
E [auth F]	IPR037002	Microviridae F protein superfamily	Homologous Superfamily
F [auth G]	IPR029053	Viral coat protein subunit	Homologous Superfamily
F [auth G]	IPR016184	Capsid/spike protein, ssDNA virus	Homologous Superfamily
F [auth G]	IPR003515	Major spike protein G	Family
G [auth B]	IPR038149	Scaffold protein B superfamily	Homologous Superfamily
G [auth B]	IPR003513	Scaffold protein B	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.