4FAE | pdb_00004fae

Substrate p2/NC in Complex with a Human Immunodeficiency Virus Type 1 Protease Variant

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	SCOP2B Superfamily	Acid proteases	8072177	3001059	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Acid proteases	8072177	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)
B	RRM_1	e4faeB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
A	adh_short_C2	e4faeA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: adh_short_C2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D]	Substrate p2/NC peptide	structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	viral gene expression viral process viral translational frameshifting viral translation virion assembly 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 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 virion component 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 virion component virion membrane host cell nucleus host cell plasma membrane host cell membrane viral nucleocapsid viral capsid
A, B	HIV-1 protease	DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity RNA-directed DNA polymerase activity catalytic activity, acting on DNA DNA polymerase activity catalytic activity, acting on a nucleic acid DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity RNA-directed DNA polymerase activity catalytic activity, acting on DNA DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding RNA stem-loop binding endonuclease activity nuclease activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	establishment of integrated proviral latency viral latency viral process establishment of viral latency proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process viral genome integration into host DNA viral life cycle	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 virion component 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 virion component virion membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
C [auth D]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
C [auth D]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
C [auth D]	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
C [auth D]	IPR001878	Zinc finger, CCHC-type	Domain
C [auth D]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
C [auth D]	IPR010999	Retroviral matrix protein	Homologous Superfamily
C [auth D]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
C [auth D]	IPR014817	Gag protein p6	Domain
C [auth D]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
A, B	IPR010661	Reverse transcriptase thumb	Domain
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B	IPR034170	Retropepsin-like catalytic domain	Domain
A, B	IPR000477	Reverse transcriptase domain	Domain
A, B	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B	IPR001969	Aspartic peptidase, active site	Active Site
A, B	IPR018061	Retropepsins	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.