4DJO | pdb_00004djo

Crystal Structure of wild-type HIV-1 Protease in Complex with MKP56

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d4djob_	All beta proteins	Acid proteases	Acid proteases	Retroviral protease (retropepsin)	Human immunodeficiency virus type 1 protease	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
A	d4djoa_	All beta proteins	Acid proteases	Acid proteases	Retroviral protease (retropepsin)	Human immunodeficiency virus type 1 protease	(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)
B	SCOP2B Superfamily	Acid proteases	8100328	3001059	SCOP2B (2022-06-29)
A	SCOP2 Family	Retroviral protease (retropepsin)	8100327	4002288	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acid proteases	8100328	3001059	SCOP2 (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	RVP	e4djoB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (1.6)
A	RVP	e4djoA1	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)
B	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.2.0)
A	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Pol polyprotein	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
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.