38OK | pdb_000038ok

AAV2 Rep68(delta1-209)/capsid/DNA complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
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)
L [auth Z]	SCOP2B Superfamily	ssDNA viruses	8041416	3000931	SCOP2B (2022-06-29)
K [auth Y]	SCOP2B Superfamily	ssDNA viruses	8041416	3000931	SCOP2B (2022-06-29)
J [auth X]	SCOP2B Superfamily	ssDNA viruses	8041416	3000931	SCOP2B (2022-06-29)
I [auth W]	SCOP2B Superfamily	ssDNA viruses	8041416	3000931	SCOP2B (2022-06-29)
H [auth V]	SCOP2B Superfamily	ssDNA viruses	8041416	3000931	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8039309	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8039309	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8039309	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8039309	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8039309	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8039309	3002019	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H [auth V], I [auth W], J [auth X], K [auth Y], L [auth Z]	PF00740	Parvovirus coat protein VP1/VP2 (VP1_2)	Parvovirus coat protein VP1/VP2	This entry describes a common domain found in VP1 and VP2 Parvovirus coat proteins which together form a capsomer. Both of these proteins are formed from the same transcript using alternative splicing. As a result, VP1 and VP2 differ only in the N-te ...	This entry describes a common domain found in VP1 and VP2 Parvovirus coat proteins which together form a capsomer. Both of these proteins are formed from the same transcript using alternative splicing. As a result, VP1 and VP2 differ only in the N-terminal. VP2 is involved in packaging of the viral DNA [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF01057	Parvovirus non-structural protein NS1 (Parvo_NS1)	Parvovirus non-structural protein NS1	This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a differen ...	This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA [2]. NS1, is the major non-structural protein. It is essential for DNA replication. It is an 83-kDa nuclear phosphoprotein. It has DNA helicase and ATPase activity [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth V], I [auth W], J [auth X], K [auth Y], L [auth Z]	Capsid protein VP1	structural molecule activity	import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of host membrane symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane disruption of anatomical structure in another organism	viral capsid icosahedral viral capsid virion component T=1 icosahedral viral capsid host intracellular membrane-bounded organelle host cellular component host intracellular part host cell nucleus other organism part host cell nucleolus host cell nuclear part host intracellular organelle cellular anatomical structure host cell part viral capsid icosahedral viral capsid virion component T=1 icosahedral viral capsid host intracellular membrane-bounded organelle host cellular component host intracellular part host cell nucleus other organism part host cell nucleolus host cell nuclear part host intracellular organelle cellular anatomical structure host cell part host intracellular region
G	ssDNA	-	-	-
A, B, C, D, E A, B, C, D, E, F	Protein Rep68	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA helicase activity macromolecular conformation isomerase activity cation binding metal ion binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process DNA biosynthetic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host cell cycle progression symbiont-mediated arrest of host cell cycle during G2/M transition modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of host membrane symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H [auth V], I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR013607	Phospholipase A2-like domain	Domain
H [auth V], I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR016184	Capsid/spike protein, ssDNA virus	Homologous Superfamily
H [auth V], I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR001403	Coat protein VP1/VP2, Parvovirus	Domain
H [auth V], I [auth W], J [auth X], K [auth Y], L [auth Z]	IPR036952	Parvovirus coat protein VP1/VP2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR014835	NS1 nuclease, NS1-Nuc domain, parvovirinae	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014015	Helicase, superfamily 3, DNA virus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR049901	NS1 nuclease, NS1-Nuc domain, Parvovirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001257	Parvovirus non-structural protein 1, helicase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily