2J9J

Atomic-resolution Crystal Structure of Chemically-Synthesized HIV-1 Protease Complexed with Inhibitor JG-365

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2j9ja_	All beta proteins	Acid proteases	Acid proteases	Retroviral protease (retropepsin)	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
B	d2j9jb_	All beta proteins	Acid proteases	Acid proteases	Retroviral protease (retropepsin)	automated matches	(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	SCOP2B Superfamily	Acid proteases	8042430	3001059	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acid proteases	8042430	3001059	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	RVP	e2j9jA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (1.6)
B	RVP	e2j9jB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
B	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00077	Retroviral aspartyl protease (RVP)	Retroviral aspartyl protease	Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a ...	Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (Pfam:PF00026).	Domain
B	PF00077	Retroviral aspartyl protease (RVP)	Retroviral aspartyl protease	Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a ...	Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (Pfam:PF00026).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROTEASE	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 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 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 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 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 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 proteolysis protein metabolic process	cellular anatomical structure 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 cellular anatomical structure 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
B	PROTEASE	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 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 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 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 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 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 proteolysis protein metabolic process	cellular anatomical structure 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 cellular anatomical structure 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
C	INHIBITOR MOLECULE JG365	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	ABA	Parent Component: ALA RESID: AA0253 , AA0409 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819
A	NLE	Parent Component: LEU RESID: AA0253 , AA0409
A	SLZ	Parent Component: LYS RESID: AA0253 , AA0409
B	ABA	Parent Component: ALA RESID: AA0253 , AA0409 , AA0253 , AA0409 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819 , S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819
B	NLE	Parent Component: LEU RESID: AA0253 , AA0409 , AA0253 , AA0409
B	SLZ	Parent Component: LYS RESID: AA0253 , AA0409 , AA0253 , AA0409
C	ACE	RESID: AA0253 , AA0409 , AA0253 , AA0409 , AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819 , S-(2-aminovinyl)-3-methyl-D-cysteine MOD:00258 , L-2-aminobutanoic acid (Glu) MOD:00819 , N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
C	JG3	RESID: AA0253 , AA0409 , AA0253 , AA0409 , AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354
C	VME	RESID: AA0253 , AA0409 , AA0253 , AA0409 , AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354