1N5Y | pdb_00001n5y

HIV-1 Reverse Transcriptase Crosslinked to Post-Translocation AZTMP-Terminated DNA (Complex P)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
F [auth H]	d1n5yh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth H]	d1n5yh2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth L]	d1n5yl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth L]	d1n5yl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth B]	d1n5yb_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Reverse transcriptase	HIV-1 reverse transcriptase	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
C [auth A]	d1n5ya1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Ribonuclease H	HIV RNase H (Domain of reverse transcriptase)	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
C [auth A]	d1n5ya2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Reverse transcriptase	HIV-1 reverse transcriptase	(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)
E [auth L]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091539	3000071	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8075088	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)
F [auth H]	Copper-bind	e1n5yH1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
E [auth L]	Copper-bind	e1n5yL1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
D [auth B]	TFR_dimer	e1n5yB1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: TFR_dimer	ECOD (develop294)
D [auth B]	RNase_P_Rpp14	e1n5yB2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
D [auth B]	Thioredoxin	e1n5yB3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (develop294)
C [auth A]	SidM_Rab1-act	e1n5yA5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: SidM_Rab1-act	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth B]	3.10.10.10	Alpha Beta	Roll	HIV Type 1 Reverse Transcriptase	Chain A, domain 1	CATH (4.3.0)
D [auth B]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
C [auth A]	3.10.10.10	Alpha Beta	Roll	HIV Type 1 Reverse Transcriptase	Chain A, domain 1	CATH (4.3.0)
C [auth A]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
C [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
F [auth H]	Fab 28	VH-CH1	Mus musculus (house mouse)	IGHV8-1201, IGHV8-501, IGHJ401, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
E [auth L]	Fab 28	L-KAPPA	Mus musculus (house mouse)	IGKV10-9401, IGKJ101, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
F [auth H]	Heavy Chain	IGHV8	-	reverse transcriptase	SAbDab (2026-03-20)
E [auth L]	Light Chain	IGKV10	Kappa	reverse transcriptase	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
E [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth H]	monoclonal antibody (heavy chain)	-	-	cellular anatomical structure extracellular region
E [auth L]	monoclonal antibody (light chain)	-	developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation response to stimulus immune response adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex plasma membrane protein complex membrane protein complex alpha-beta T cell receptor complex receptor complex plasma membrane signaling receptor complex T cell receptor complex extracellular region IgG immunoglobulin complex immunoglobulin complex
D [auth B]	REVERSE TRANSCRIPTASE	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 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, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity RNA endonuclease activity 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 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 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 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 cellular 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 biological 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 regulation of killing of cells of another organism disruption of cell in another organism regulation of cell killing symbiont-mediated perturbation of host apoptosis disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure 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
C [auth A]	REVERSE TRANSCRIPTASE	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 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, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity RNA endonuclease activity 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 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 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 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 cellular 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 biological 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 regulation of killing of cells of another organism disruption of cell in another organism regulation of cell killing symbiont-mediated perturbation of host apoptosis disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure 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
B [auth P]	5'-D(ACPAPGPTPCPCPCPTPGPTPTPCPGPGP(MRG)PCPGPCPCP*(ATM))-3'	-	-	-
A [auth T]	5'-D(APTPGPCTPAPGPGPCPGPCPCPCPGPAPAPCPAPGPGPGPAPCPTPGPTP*G)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth H]	IPR003597	Immunoglobulin C1-set	Domain
F [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
F [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
F [auth H]	IPR007110	Immunoglobulin-like domain	Domain
F [auth H]	IPR050380	Immune Recognition and Response Modulators	Family
E [auth L]	IPR003597	Immunoglobulin C1-set	Domain
E [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth L]	IPR007110	Immunoglobulin-like domain	Domain
E [auth L]	IPR050380	Immune Recognition and Response Modulators	Family
E [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
D [auth B]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
D [auth B]	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
D [auth B]	IPR001878	Zinc finger, CCHC-type	Domain
D [auth B]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
D [auth B]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
D [auth B]	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
D [auth B]	IPR018061	Retropepsins	Domain
D [auth B]	IPR010661	Reverse transcriptase thumb	Domain
D [auth B]	IPR002156	Ribonuclease H domain	Domain
D [auth B]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
D [auth B]	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
D [auth B]	IPR001584	Integrase, catalytic core	Domain
D [auth B]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
D [auth B]	IPR010999	Retroviral matrix protein	Homologous Superfamily
D [auth B]	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
D [auth B]	IPR001969	Aspartic peptidase, active site	Active Site
D [auth B]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
D [auth B]	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
D [auth B]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
D [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
D [auth B]	IPR001037	Integrase, C-terminal, retroviral	Domain
D [auth B]	IPR034170	Retropepsin-like catalytic domain	Domain
D [auth B]	IPR000477	Reverse transcriptase domain	Domain
D [auth B]	IPR010659	Reverse transcriptase connection	Domain
D [auth B]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
C [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth A]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C [auth A]	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
C [auth A]	IPR001878	Zinc finger, CCHC-type	Domain
C [auth A]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
C [auth A]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
C [auth A]	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
C [auth A]	IPR018061	Retropepsins	Domain
C [auth A]	IPR010661	Reverse transcriptase thumb	Domain
C [auth A]	IPR002156	Ribonuclease H domain	Domain
C [auth A]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
C [auth A]	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
C [auth A]	IPR001584	Integrase, catalytic core	Domain
C [auth A]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
C [auth A]	IPR010999	Retroviral matrix protein	Homologous Superfamily
C [auth A]	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
C [auth A]	IPR001969	Aspartic peptidase, active site	Active Site
C [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C [auth A]	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
C [auth A]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
C [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth A]	IPR001037	Integrase, C-terminal, retroviral	Domain
C [auth A]	IPR034170	Retropepsin-like catalytic domain	Domain
C [auth A]	IPR000477	Reverse transcriptase domain	Domain
C [auth A]	IPR010659	Reverse transcriptase connection	Domain
C [auth A]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily