1CD3 | pdb_00001cd3

PROCAPSID OF BACTERIOPHAGE PHIX174

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth F]	SCOP2B Superfamily	ssDNA viruses	8040766	3000931	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)
A [auth 1]	SCOP2B Superfamily	Scaffolding protein gpD of bacteriophage procapsid	8032652	3000749	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)
G [auth B]		e1cd3B1	A: Scaffolding protein GPB	X: Scaffolding protein GPB	H: Scaffolding protein GPB	T: Phage_B	F:	ECOD (20:10:01)
F [auth G]		e1cd3G1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Rhv	F:	ECOD (20:10:01)
E [auth F]		e1cd3F1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Rhv	F:	ECOD (20:10:01)
B [auth 2]		e1cd321	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
C [auth 3]		e1cd331	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
D [auth 4]		e1cd342	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: Trypsin_2	F:	ECOD (20:10:01)
A [auth 1]		e1cd311	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
F [auth G]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		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)
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)
A [auth 1]	1.10.1850.10	Mainly Alpha	Orthogonal Bundle	Procapsid Of Bacteriophage Phix174, Chain 1	Scaffold protein D	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 proteolysis metabolic process cellular 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 cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part
F [auth G]	PROTEIN (SPIKE PROTEIN GPG)	-	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host process modulation of process of another organism symbiont entry into host cell symbiont entry into host	viral capsid virion component host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part
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
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 cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth B]	IPR038149	Scaffold protein B superfamily	Homologous Superfamily
G [auth B]	IPR003513	Scaffold protein B	Family
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
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
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

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.