1K6Y

Crystal Structure of a Two-Domain Fragment of HIV-1 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	d1k6ya1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Retroviral integrase, N-terminal Zn binding domain	HIV/SIV integrase, N-terminal Zn binding domain	N-terminal Zn binding domain of HIV integrase	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
A	d1k6ya2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	Retroviral integrase, catalytic domain	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
B	d1k6yb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Retroviral integrase, N-terminal Zn binding domain	HIV/SIV integrase, N-terminal Zn binding domain	N-terminal Zn binding domain of HIV integrase	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
B	d1k6yb2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	Retroviral integrase, catalytic domain	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
C	d1k6yc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Retroviral integrase, N-terminal Zn binding domain	HIV/SIV integrase, N-terminal Zn binding domain	N-terminal Zn binding domain of HIV integrase	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
C	d1k6yc2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	Retroviral integrase, catalytic domain	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
D	d1k6yd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Retroviral integrase, N-terminal Zn binding domain	HIV/SIV integrase, N-terminal Zn binding domain	N-terminal Zn binding domain of HIV integrase	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
D	d1k6yd2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	Retroviral integrase, catalytic domain	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	N-terminal Zn binding domain of HIV integrase	8025468	4000740	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	N-terminal Zn binding domain of HIV integrase-like	8037847	3001203	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8037847	3001203	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8037847	3001203	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8037847	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	Integrase_Zn	e1k6yA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
A	rve	e1k6yA2	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	Integrase_Zn	e1k6yB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
B	rve	e1k6yB2	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	Integrase_Zn	e1k6yC1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
C	rve	e1k6yC2	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	Integrase_Zn	e1k6yD1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
D	rve	e1k6yD2	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)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	Integrase	catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity lipid binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters RNA-DNA hybrid ribonuclease activity RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell viral process symbiont entry into host viral life cycle viral genome integration into host DNA symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell viral process symbiont entry into host viral life cycle viral genome integration into host DNA viral penetration into host nucleus intracellular transport of virus transport of virus nucleobase-containing compound metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation DNA recombination regulation of cellular process symbiont-mediated activation of host programmed cell death symbiont-mediated activation of host apoptosis positive regulation of killing of cells of another organism positive regulation of biological process regulation of programmed cell death regulation of killing of cells of another organism disruption of cell in another organism symbiont-mediated perturbation of host apoptosis positive regulation of cellular process killing of cells of another organism regulation of biological process positive regulation of programmed cell death symbiont-mediated perturbation of host programmed cell death regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process regulation of cell killing apoptotic process positive regulation of cell killing disruption of anatomical structure in another organism programmed cell death symbiont-mediated killing of host cell cell killing proteolysis protein metabolic process	membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid viral capsid virion component host cell plasma membrane host cell membrane host cell virion membrane host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B, C, D	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C, D	IPR018061	Retropepsins	Domain
A, B, C, D	IPR010661	Reverse transcriptase thumb	Domain
A, B, C, D	IPR002156	Ribonuclease H domain	Domain
A, B, C, D	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C, D	IPR001584	Integrase, catalytic core	Domain
A, B, C, D	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C, D	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A, B, C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, C, D	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D	IPR010659	Reverse transcriptase connection	Domain
A, B, C, D	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily