5DCX

Structural studies of AAV2 Rep68 reveal a partially structured linker and compact domain conformation

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
A	d5dcxa1	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
A	d5dcxa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
B	d5dcxb1	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
B	d5dcxb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
C	d5dcxc_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
D	d5dcxd_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
E	d5dcxe_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
F	d5dcxf_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
G	d5dcxg_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
H	d5dcxh_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
I	d5dcxi_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
J	d5dcxj_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)
K	d5dcxk_	Alpha and beta proteins (a+b)	Origin of replication-binding domain, RBD-like	Origin of replication-binding domain, RBD-like	Replication protein Rep, nuclease domain	automated matches	AAV-2 (adeno-associated virus 2 ) [TaxId: 10804 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
D	SCOP2 Family	Replication protein Rep nuclease domain	8089615	4002726	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Origin of replication-binding domain RBD-like	8089616	3001937	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	PF08724	e5dcxA1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
B	PF08724	e5dcxB1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
C	PF08724	e5dcxC1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
D	PF08724	e5dcxD1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
E	PF08724	e5dcxE1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
F	PF08724	e5dcxF1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
G	PF08724	e5dcxG1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
H	PF08724	e5dcxH1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
I	PF08724	e5dcxI1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
J	PF08724	e5dcxJ1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)
K	PF08724	e5dcxK1	A: a+b two layers	X: Alpha-beta plaits	H: Origin of replication-binding domains	T: Origin of replication-binding domains	F: PF08724	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
B	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
C	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
D	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
E	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
F	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
G	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
H	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
I	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
J	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)
K	3.40.1310.20	Alpha Beta	3-Layer(aba) Sandwich	Replication Protein E1	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	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
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	PF08724	Rep protein catalytic domain like (Rep_N)	Rep protein catalytic domain like	Adeno-associated virus (AAV) Replication (Rep) protein is essential for viral replication and integration. The catalytic domain has DNA binding and endonuclease activity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	Protein Rep68	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 hydrolase activity, acting on ester bonds cation binding metal ion binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process symbiont-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of inner membrane biological process involved in interspecies interaction between organisms symbiont entry into host cell via permeabilization of host membrane viral life cycle nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process symbiont-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of inner membrane biological process involved in interspecies interaction between organisms symbiont entry into host cell via permeabilization of host membrane viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host membrane symbiont-mediated disruption of host cellular anatomical entity symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism cellular biosynthetic process cellular metabolic process viral DNA genome replication nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication organic cyclic compound biosynthetic process organic substance biosynthetic process cellular process DNA biosynthetic process permeabilization of host organelle membrane involved in viral entry into host cell symbiont-mediated perturbation of host cellular process modulation by symbiont of host process symbiont-mediated perturbation of host cell cycle progression symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint modulation of process of another organism symbiont-mediated arrest of host cell cycle during G2/M transition	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus host intracellular organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	IPR014835	NS1 nuclease, NS1-Nuc domain, parvovirinae	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	IPR014015	Helicase, superfamily 3, DNA virus	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	IPR001257	Parvovirus non-structural protein 1, helicase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

RCSB PDB Core Operations are 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.