3QIN

Crystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol carboxylic acid inhibitor

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	d3qina1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Ribonuclease H	HIV RNase H (Domain of reverse transcriptase)	HIV-1 (HIV-1 M:B_HXB2R ) [TaxId: 11706 ], (Escherichia coli K-12 ) [TaxId: 83333 ], HIV-1 (HIV-1 M:B_HXB2R ) [TaxId: 11706 ],	SCOPe (2.08)
A	d3qina2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HIV-1 (HIV-1 M:B_HXB2R ) [TaxId: 11706 ], (Escherichia coli K-12 ) [TaxId: 83333 ], HIV-1 (HIV-1 M:B_HXB2R ) [TaxId: 11706 ],	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	8044518	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)
A	RNase_H	e3qinA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_H	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00075	RNase H (RNase_H)	RNase H	RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Fusion protein of HIV-1 RNase H p15 with engineered E. coli loop	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity nuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase 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 catalytic activity organic cyclic compound binding nucleic acid binding RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters exoribonuclease H activity exonuclease 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 RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding identical protein binding protein binding peptidase activity catalytic activity, acting on a protein integrase activity aspartic-type peptidase activity aspartic-type endopeptidase activity endopeptidase activity lipid binding structural molecule activity transition metal ion binding zinc ion binding	DNA replication, removal of RNA primer catabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA replication nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA replication, removal of RNA primer catabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA replication nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral process viral life cycle symbiont entry into host cell symbiont entry into host viral genome integration into host DNA viral penetration into host nucleus intracellular transport of virus transport of virus establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process DNA recombination regulation of biological process symbiont-mediated perturbation of host cellular process symbiont-mediated activation of host programmed cell death regulation of cellular process symbiont-mediated activation of host apoptosis symbiont-mediated perturbation of host programmed cell death biological regulation disruption of cell in another organism regulation of killing of cells of another organism regulation of cell killing disruption of anatomical structure in another organism symbiont-mediated perturbation of host apoptosis symbiont-mediated killing of host cell killing of cells of another organism cell killing	cellular anatomical structure intracellular anatomical structure cytoplasm membrane 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 cellular anatomical structure intracellular anatomical structure cytoplasm membrane 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	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR022892	Ribonuclease HI	Family
A	IPR002156	Ribonuclease H domain	Domain
A	IPR050092	Ribonuclease H	Family
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A	IPR001878	Zinc finger, CCHC-type	Domain
A	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A	IPR018061	Retropepsins	Domain
A	IPR010661	Reverse transcriptase thumb	Domain
A	IPR002156	Ribonuclease H domain	Domain
A	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A	IPR001584	Integrase, catalytic core	Domain
A	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A	IPR010999	Retroviral matrix protein	Homologous Superfamily
A	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A	IPR001969	Aspartic peptidase, active site	Active Site
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR001037	Integrase, C-terminal, retroviral	Domain
A	IPR034170	Retropepsin-like catalytic domain	Domain
A	IPR000477	Reverse transcriptase domain	Domain
A	IPR010659	Reverse transcriptase connection	Domain
A	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily