Annotations: 6SA9

Endogenous Retrovirus HML2 Capsid NTD

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	MG4	e6sa9B1	A: beta barrels	X: jelly-roll	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (v294.2)
A	MG4	e6sa9A1	A: beta barrels	X: jelly-roll	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: MG4	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00607	gag protein p24 N-terminal domain (Gag_p24)	gag protein p24 N-terminal domain	p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Endogenous retrovirus group K member 9 Pol protein	RNA binding binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein RNA binding binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity endopeptidase activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity RNA-directed DNA polymerase activity structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	viral gene expression viral process viral translational frameshifting viral translation proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B	IPR036157	dUTPase-like superfamily	Homologous Superfamily
A, B	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B	IPR038124	Beta-retroviral matrix superfamily	Homologous Superfamily
A, B	IPR003322	Beta-retroviral matrix protein	Domain
A, B	IPR001878	Zinc finger, CCHC-type	Domain
A, B	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B	IPR001969	Aspartic peptidase, active site	Active Site
A, B	IPR029054	dUTPase-like	Domain
A, B	IPR000467	G-patch domain	Domain
A, B	IPR018061	Retropepsins	Domain
A, B	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR033704	dUTPase, trimeric	Domain
A, B	IPR034170	Retropepsin-like catalytic domain	Domain
A, B	IPR000477	Reverse transcriptase domain	Domain
A, B	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

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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.

6SA9 | pdb_00006sa9

Endogenous Retrovirus HML2 Capsid NTD

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage