Annotations: 4PH0

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ph0a2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
A	d4ph0a1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
B	d4ph0b2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
B	d4ph0b1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
C	d4ph0c2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
C	d4ph0c1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
D	d4ph0d2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
D	d4ph0d1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
E	d4ph0e2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
E	d4ph0e1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
F	d4ph0f2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
F	d4ph0f1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	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	PF19317	e4ph0A1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: PF19317	ECOD (1.6)
A	PF00607	e4ph0A2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: PF00607	ECOD (1.6)
B	PF19317	e4ph0B2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: PF19317	ECOD (1.6)
B	PF00607	e4ph0B1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: PF00607	ECOD (1.6)
C	PF19317	e4ph0C2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: PF19317	ECOD (1.6)
C	PF00607	e4ph0C1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: PF00607	ECOD (1.6)
D	PF19317	e4ph0D1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: PF19317	ECOD (1.6)
D	PF00607	e4ph0D2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: PF00607	ECOD (1.6)
E	PF19317	e4ph0E1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: PF19317	ECOD (1.6)
E	PF00607	e4ph0E2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: PF00607	ECOD (1.6)
F	PF19317	e4ph0F1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: PF19317	ECOD (1.6)
F	PF00607	e4ph0F2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: PF00607	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
A	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
B	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
B	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
C	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
C	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
D	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
D	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
E	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
E	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
F	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
F	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF19317	Gag protein p24 C-terminal domain (Gag_p24_C)	Gag protein p24 C-terminal domain	p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	BLV capsid	DNA binding binding organic cyclic compound binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA DNA binding binding organic cyclic compound binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters RNA-directed DNA polymerase activity catalytic activity, acting on DNA DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	establishment of integrated proviral latency viral latency viral process establishment of viral latency viral genome integration into host DNA viral life cycle nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process establishment of integrated proviral latency viral latency viral process establishment of viral latency viral genome integration into host DNA viral life cycle nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction DNA integration organonitrogen compound metabolic process proteolysis protein metabolic process	viral nucleocapsid viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003139	Delta-retroviral matrix protein	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR018061	Retropepsins	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002156	Ribonuclease H domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001584	Integrase, catalytic core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

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.