3VQ9 | pdb_00003vq9

HIV-1 IN core domain in complex with 6-fluoro-1,3-benzothiazol-2-amine

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)
C	d3vq9c_	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	d3vq9b_	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)
A	d3vq9a_	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)
C	SCOP2 Family	Retroviral integrase, catalytic domain	8077041	4000539	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ribonuclease H-like	8077042	3000143	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8077042	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8077042	3000143	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)
C	rve	e3vq9C1	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	rve	e3vq9B2	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)
A	rve	e3vq9A2	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)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	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	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	POL polyprotein	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 hydrolase activity, acting on ester bonds nuclease activity exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity 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 hydrolase activity, acting on ester bonds nuclease activity 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 nucleic acid 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, hydrolytic mechanism RNA-DNA hybrid ribonuclease 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	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 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 establishment of integrated proviral latency viral latency 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 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 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 viral penetration into host nucleus intracellular transport of virus transport of virus DNA integration proteolysis protein metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host cell host intracellular membrane-bounded organelle host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host cell host intracellular membrane-bounded organelle host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell late endosome host cell endosome host intracellular region virion component virion membrane host cell nucleus viral nucleocapsid viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C	IPR018061	Retropepsins	Domain
A, B, C	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C	IPR010661	Reverse transcriptase thumb	Domain
A, B, C	IPR002156	Ribonuclease H domain	Domain
A, B, C	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C	IPR001584	Integrase, catalytic core	Domain
A, B, C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, C	IPR000477	Reverse transcriptase domain	Domain
A, B, C	IPR010659	Reverse transcriptase connection	Domain

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 R01GM157729.