4PWD

Crystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA and Nevirapine

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	d4pwda2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	HIV-1 (Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	SCOPe (2.08)
A	d4pwda1	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Reverse transcriptase	automated matches	HIV-1 (Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	SCOPe (2.08)
A	d4pwda3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HIV-1 (Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	SCOPe (2.08)
C	d4pwdc2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	HIV-1 (Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	SCOPe (2.08)
C	d4pwdc1	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Reverse transcriptase	automated matches	HIV-1 (Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	SCOPe (2.08)
C	d4pwdc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HIV-1 (Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	SCOPe (2.08)
B	d4pwdb_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Reverse transcriptase	HIV-1 reverse transcriptase	HIV-1 (Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	SCOPe (2.08)
D	d4pwdd_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Reverse transcriptase	HIV-1 reverse transcriptase	HIV-1 (Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	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	8075088	3000143	SCOP2B (2022-06-29)
C	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)
A	RVT_thumb	e4pwdA3	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: RVT_thumb	ECOD (1.6)
A	RVT_1	e4pwdA4	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RVT_1	ECOD (1.6)
A	RNase_H	e4pwdA2	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)
A	RVT_connect	e4pwdA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: RNaseH-like domain in reverse transcriptase (From Topology)	T: RNaseH-like domain in reverse transcriptase	F: RVT_connect	ECOD (1.6)
C	RVT_thumb	e4pwdC3	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: RVT_thumb	ECOD (1.6)
C	RVT_1	e4pwdC4	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RVT_1	ECOD (1.6)
C	RNase_H	e4pwdC2	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)
C	RVT_connect	e4pwdC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: RNaseH-like domain in reverse transcriptase (From Topology)	T: RNaseH-like domain in reverse transcriptase	F: RVT_connect	ECOD (1.6)
B	RVT_thumb	e4pwdB2	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: RVT_thumb	ECOD (1.6)
B	RVT_1	e4pwdB1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RVT_1	ECOD (1.6)
B	RVT_connect	e4pwdB3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: RNaseH-like domain in reverse transcriptase (From Topology)	T: RNaseH-like domain in reverse transcriptase	F: RVT_connect	ECOD (1.6)
D	RVT_thumb	e4pwdD2	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: RVT_thumb	ECOD (1.6)
D	RVT_1	e4pwdD1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RVT_1	ECOD (1.6)
D	RVT_connect	e4pwdD3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: RNaseH-like domain in reverse transcriptase (From Topology)	T: RNaseH-like domain in reverse transcriptase	F: RVT_connect	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.10.10	Alpha Beta	Roll	HIV Type 1 Reverse Transcriptase	Chain A, domain 1	CATH (4.3.0)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.10.10.10	Alpha Beta	Roll	HIV Type 1 Reverse Transcriptase	Chain A, domain 1	CATH (4.3.0)
C	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.10.10.10	Alpha Beta	Roll	HIV Type 1 Reverse Transcriptase	Chain A, domain 1	CATH (4.3.0)
B	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
D	3.10.10.10	Alpha Beta	Roll	HIV Type 1 Reverse Transcriptase	Chain A, domain 1	CATH (4.3.0)
D	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF06817	Reverse transcriptase thumb domain (RVT_thumb)	Reverse transcriptase thumb domain	This domain is known as the thumb domain. It is composed of a four helix bundle [1].	Domain
A, C	PF06815	Reverse transcriptase connection domain (RVT_connect)	Reverse transcriptase connection domain	This domain is known as the connection domain. This domain lies between the thumb and palm domains [1].	Domain
A, C	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
A, C	PF00078	Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)	Reverse transcriptase (RNA-dependent DNA polymerase)	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ...	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.	Domain
B, D	PF06817	Reverse transcriptase thumb domain (RVT_thumb)	Reverse transcriptase thumb domain	This domain is known as the thumb domain. It is composed of a four helix bundle [1].	Domain
B, D	PF06815	Reverse transcriptase connection domain (RVT_connect)	Reverse transcriptase connection domain	This domain is known as the connection domain. This domain lies between the thumb and palm domains [1].	Domain
B, D	PF00078	Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)	Reverse transcriptase (RNA-dependent DNA polymerase)	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ...	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	HIV-1 Reverse Transcriptase, P66 subunit	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
B, D	HIV-1 Reverse Transcriptase, P51 subunit	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
E [auth T], F [auth E]	5'-R(APUPGPGPUPCPGPGPCPGPCPCPCPGPAPAPAPCPAPGPGPGPAPCPUPGP*U)-3'	-	-	-
G [auth P], H [auth F]	5'-D(ACPAPGPTPCPCPCPTPGPTPTPCPGPGPGPCPGPCPCP*G)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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