6VKA

HIV Integrase Core domain (IN) in complex with dimer-spanning ligand

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d6vkaa_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	Retroviral integrase, catalytic domain	HIV-1 (Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
B	d6vkab_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	Retroviral integrase, catalytic domain	HIV-1 (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	Ribonuclease H-like	8077044	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8077044	3000143	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	rve	e6vkaA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
B	rve	e6vkaB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Integrase	DNA binding binding organic cyclic compound binding nucleic acid binding RNA-directed DNA polymerase activity catalytic activity, acting on DNA DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding RNA stem-loop binding DNA binding binding organic cyclic compound binding nucleic acid binding RNA-directed DNA polymerase activity catalytic activity, acting on DNA DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding RNA stem-loop binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process DNA recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B	IPR001584	Integrase, catalytic core	Domain
A, B	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.