Annotations: 3JCA

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8072149	3001203	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8072149	3001203	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8072149	3001203	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8072149	3001203	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	IN_DBD_C	e3jcaA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
A	Integrase_Zn	e3jcaA3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
A	rve	e3jcaA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
B	IN_DBD_C	e3jcaB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
B	Integrase_Zn	e3jcaB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
B	rve	e3jcaB3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
E	IN_DBD_C	e3jcaE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
E	Integrase_Zn	e3jcaE2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
E	rve	e3jcaE3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
F	IN_DBD_C	e3jcaF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
F	Integrase_Zn	e3jcaF3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
F	rve	e3jcaF2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
C	IN_DBD_C	e3jcaC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
D	IN_DBD_C	e3jcaD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
G	IN_DBD_C	e3jcaG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
H	IN_DBD_C	e3jcaH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E, F	PF02022	Integrase Zinc binding domain (Integrase_Zn)	Integrase Zinc binding domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665 ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. The carboxyl terminal domain is a DNA binding domain Pfam:PF00552.	Domain
A, B, E, F	PF00552	Integrase DNA binding domain (IN_DBD_C)	Integrase DNA binding domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This do ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain [1].	Domain
A, B, E, F	PF00665	Integrase core domain (rve)	Integrase core domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The ca ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site [1].	Domain
C, D, G, H	PF00552	Integrase DNA binding domain (IN_DBD_C)	Integrase DNA binding domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This do ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E, F	Integrase	RNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding aspartic-type peptidase activity RNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity endopeptidase activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity 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 pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides dUTP diphosphatase activity hydrolase activity, acting on acid anhydrides structural constituent of virion structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	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 establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA 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 establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA nucleobase-containing compound metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA integration proteolysis protein metabolic process	viral nucleocapsid viral capsid virion component
C, D, G, H	Integrase	RNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding aspartic-type peptidase activity RNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity endopeptidase activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity 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 pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides dUTP diphosphatase activity hydrolase activity, acting on acid anhydrides structural constituent of virion structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	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 establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA 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 establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA nucleobase-containing compound metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA integration proteolysis protein metabolic process	viral nucleocapsid viral capsid virion component
I, K	5'-D(APAPTPGPCPCPGPCPAPGPTPCPGPGPCPCPGPAPCPCPTPG)-3'	-	-	-
J, L	5'-D(CPAPGPGPTPCPGPGPCPCPGPAPCPTPGPCPGPGPCPA)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E, F	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, E, F	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, E, F	IPR036157	dUTPase-like superfamily	Homologous Superfamily
A, B, E, F	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, E, F	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, E, F	IPR038124	Beta-retroviral matrix superfamily	Homologous Superfamily
A, B, E, F	IPR003322	Beta-retroviral matrix protein	Domain
A, B, E, F	IPR001878	Zinc finger, CCHC-type	Domain
A, B, E, F	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, E, F	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, E, F	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, E, F	IPR001969	Aspartic peptidase, active site	Active Site
A, B, E, F	IPR029054	dUTPase-like	Domain
A, B, E, F	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, E, F	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, E, F	IPR018061	Retropepsins	Domain
A, B, E, F	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, E, F	IPR010661	Reverse transcriptase thumb	Domain
A, B, E, F	IPR002156	Ribonuclease H domain	Domain
A, B, E, F	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, E, F	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, E, F	IPR001584	Integrase, catalytic core	Domain
A, B, E, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, E, F	IPR033704	dUTPase, trimeric	Domain
A, B, E, F	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, E, F	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, E, F	IPR000477	Reverse transcriptase domain	Domain
A, B, E, F	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
C, D, G, H	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C, D, G, H	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
C, D, G, H	IPR036157	dUTPase-like superfamily	Homologous Superfamily
C, D, G, H	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C, D, G, H	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
C, D, G, H	IPR038124	Beta-retroviral matrix superfamily	Homologous Superfamily
C, D, G, H	IPR003322	Beta-retroviral matrix protein	Domain
C, D, G, H	IPR001878	Zinc finger, CCHC-type	Domain
C, D, G, H	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
C, D, G, H	IPR010999	Retroviral matrix protein	Homologous Superfamily
C, D, G, H	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
C, D, G, H	IPR001969	Aspartic peptidase, active site	Active Site
C, D, G, H	IPR029054	dUTPase-like	Domain
C, D, G, H	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
C, D, G, H	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C, D, G, H	IPR018061	Retropepsins	Domain
C, D, G, H	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
C, D, G, H	IPR010661	Reverse transcriptase thumb	Domain
C, D, G, H	IPR002156	Ribonuclease H domain	Domain
C, D, G, H	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
C, D, G, H	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
C, D, G, H	IPR001584	Integrase, catalytic core	Domain
C, D, G, H	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C, D, G, H	IPR033704	dUTPase, trimeric	Domain
C, D, G, H	IPR001037	Integrase, C-terminal, retroviral	Domain
C, D, G, H	IPR034170	Retropepsin-like catalytic domain	Domain
C, D, G, H	IPR000477	Reverse transcriptase domain	Domain
C, D, G, H	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily