7JN3 | pdb_00007jn3

Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048

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)
H	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	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)
H	V-set	e7jn3H1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)
G	V-set	e7jn3G1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)
F	V-set	e7jn3F1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)
E	V-set	e7jn3E1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)
D	V-set	e7jn3D1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)
C	V-set	e7jn3C1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)
B	V-set	e7jn3B1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.1)
A	DctP	e7jn3A1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
E	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
A	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J, L	DNA (5'-D(APTPTPGPCPAPTPAPAPGPAPCPAPAPCPA)-3')	-	-	-
I, K	DNA (5'-D(APAPTPGPTPTPGPTPCPTPTPAPTPGPCPAPAPT)-3')	-	-	-
A, B, C, D, E A, B, C, D, E, F, G, H	integrase	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 binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein 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 binding nucleic acid 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, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding 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 cellular 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018061	Retropepsins	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010661	Reverse transcriptase thumb	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004028	Retroviral Gag polyprotein, M	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002156	Ribonuclease H domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001584	Integrase, catalytic core	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily