5CZ2

Crystal structure of a two-domain fragment of MMTV integrase

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)
A	d5cz2a_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	MMTV (Mouse mammary tumor virus (STRAIN BR6) ) [TaxId: 11758 ],	SCOPe (2.08)
C	d5cz2c_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	MMTV (Mouse mammary tumor virus (STRAIN BR6) ) [TaxId: 11758 ],	SCOPe (2.08)
D	d5cz2d_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	MMTV (Mouse mammary tumor virus (STRAIN BR6) ) [TaxId: 11758 ],	SCOPe (2.08)
E	d5cz2e_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	MMTV (Mouse mammary tumor virus (STRAIN BR6) ) [TaxId: 11758 ],	SCOPe (2.08)
B	d5cz2b_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	MMTV (Mouse mammary tumor virus (STRAIN BR6) ) [TaxId: 11758 ],	SCOPe (2.08)

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)
C	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
H	SCOP2 Family	N-terminal Zn binding domain of HIV integrase	8072148	4000740	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	N-terminal Zn binding domain of HIV integrase-like	8072149	3001203	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8072149	3001203	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8072149	3001203	SCOP2B (2022-06-29)
L	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)
G	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8072149	3001203	SCOP2B (2022-06-29)
K	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	rve	e5cz2A1	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	rve	e5cz2C1	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)
D	rve	e5cz2D1	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	rve	e5cz2E1	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	rve	e5cz2F1	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)
H	Integrase_Zn	e5cz2H1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
I	Integrase_Zn	e5cz2I1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
J	Integrase_Zn	e5cz2J1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
L	Integrase_Zn	e5cz2L1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
B	rve	e5cz2B1	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)
G	Integrase_Zn	e5cz2G1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
K	Integrase_Zn	e5cz2K1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
H	1.10.10.200	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Integrase, N-terminal zinc-binding domain	CATH (4.3.0)
J	1.10.10.200	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Integrase, N-terminal zinc-binding domain	CATH (4.3.0)
L	1.10.10.200	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Integrase, N-terminal zinc-binding domain	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
G	1.10.10.200	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Integrase, N-terminal zinc-binding domain	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, G, H, I, J, K, L	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

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