3AVK

Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site

Domain Annotation: CATH CATH Database (version 4.2.0) Homepage

Chain	Domain	Class	Architecture	Topology	Homology
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
A, B	PF06817	Reverse transcriptase thumb domain (RVT_thumb)	Reverse transcriptase thumb domain	This domain is known as the thumb domain. It is composed of a four helix bundle [1].	Domain
A, B	PF06815	Reverse transcriptase connection domain (RVT_connect)	Reverse transcriptase connection domain	This domain is known as the connection domain. This domain lies between the thumb and palm domains [1].	Domain
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
A, B	PF00075	RNase H (RNase_H)	RNase H	RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.	Domain
A, B	PF02022	Integrase Zinc binding domain (Integrase_Zn)	Integrase Zinc binding domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665 ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. The carboxyl terminal domain is a DNA binding domain Pfam:PF00552.	Domain
A, B	PF00098	Zinc knuckle (zf-CCHC)	Zinc knuckle	The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eu ...	The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.	Domain
A, B	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
A, B	PF00540	gag gene protein p17 (matrix protein) (Gag_p17)	gag gene protein p17 (matrix protein)	The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.	Domain
A, B	PF00078	Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)	Reverse transcriptase (RNA-dependent DNA polymerase)	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ...	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.	Domain
A, B	PF00552	Integrase DNA binding domain (IN_DBD_C)	Integrase DNA binding domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This do ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain [1].	Domain
A, B	PF00665	Integrase core domain (rve)	Integrase core domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The ca ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site [1].	Domain

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Integrase	catalytic activity endopeptidase activity aspartic-type endopeptidase activity peptidase activity hydrolase activity aspartic-type peptidase activity catalytic activity, acting on a protein nucleic acid binding DNA binding binding organic cyclic compound binding heterocyclic compound binding DNA-directed DNA polymerase activity transferase activity transferase activity, transferring phosphorus-containing groups nucleotidyltransferase activity DNA polymerase activity catalytic activity, acting on DNA nuclease activity exonuclease activity exoribonuclease activity exoribonuclease H activity ribonuclease activity hydrolase activity, acting on ester bonds exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters exoribonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA protein binding identical protein binding lipid binding phospholipid binding phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol binding ion binding anion binding phosphatidylinositol phosphate binding phosphatidylinositol bisphosphate binding RNA binding RNA-directed DNA polymerase activity endonuclease activity endoribonuclease activity RNA-DNA hybrid ribonuclease activity endoribonuclease activity, producing 5'-phosphomonoesters endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters structural molecule activity zinc ion binding cation binding metal ion binding transition metal ion binding	viral process viral latency establishment of viral latency biological process involved in symbiotic interaction biological process involved in interspecies interaction between organisms establishment of integrated proviral latency metabolic process negative regulation of metabolic process gene expression regulation of gene expression negative regulation of macromolecule metabolic process negative regulation of gene expression modulation by virus of host process regulation of metabolic process modulation of process of other organism modulation by virus of host gene expression suppression by virus of host gene expression macromolecule metabolic process modulation by symbiont of host process negative regulation of biological process regulation of biological process biological process involved in interaction with host modulation of process of other organism involved in symbiotic interaction regulation of macromolecule metabolic process biological regulation organic substance metabolic process viral life cycle entry into host viral entry into host cell movement in host environment viral genome integration into host DNA	host cellular component host cell part host intracellular part host intracellular organelle host intracellular membrane-bounded organelle host cell nucleus host intracellular region host cell cellular anatomical entity host cell plasma membrane host cell membrane host cell cytoplasm host cell cytoplasm part host cell endosome host cell late endosome host multivesicular body virion viral nucleocapsid viral capsid virion part membrane virion membrane
D, F	LEDGF peptide	none	none	none

RCSB PDB is 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.