4QJ2

Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with WT p1-p6 substrate

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Acid proteases	8098148	3001059	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Acid proteases	8098148	3001059	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Acid proteases	8098148	3001059	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acid proteases	8098148	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)
C	RVP	e4qj2C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (1.6)
D	RVP	e4qj2D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (1.6)
A	RVP	e4qj2A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (1.6)
B	RVP	e4qj2B1	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)
C	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
D	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
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, B, C, D	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
E [auth F], F [auth G]	PF08705	Gag protein p6 (Gag_p6)	Gag protein p6	HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors ...	HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors [1]. The PTAP motif interacts with the cellular budding factor TSG101 [1]. This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Protease	aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	-
E [auth F], F [auth G]	p1-p6 peptide	structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding organic cyclic compound binding nucleic acid binding	virion assembly viral process viral budding viral budding via host ESCRT complex viral life cycle	host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region membrane virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region membrane virion component virion membrane host cell nuclear membrane host cell membrane host cell nucleus host cell nuclear part host cell endomembrane system host cell nuclear envelope host cell plasma membrane viral nucleocapsid viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, C, D	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D	IPR018061	Retropepsins	Domain
E [auth F], F [auth G]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
E [auth F], F [auth G]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
E [auth F], F [auth G]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
E [auth F], F [auth G]	IPR001878	Zinc finger, CCHC-type	Domain
E [auth F], F [auth G]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
E [auth F], F [auth G]	IPR010999	Retroviral matrix protein	Homologous Superfamily
E [auth F], F [auth G]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
E [auth F], F [auth G]	IPR014817	Gag protein p6	Domain
E [auth F], F [auth G]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.