5DCX | pdb_00005dcx

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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	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)
I	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)
G	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)
E	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)
C	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)
A	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)
K	Piezo_RRas_bdg	e5dcxK1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
J	Piezo_RRas_bdg	e5dcxJ1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
I	Piezo_RRas_bdg	e5dcxI1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
H	Piezo_RRas_bdg	e5dcxH1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
G	Piezo_RRas_bdg	e5dcxG1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
F	Piezo_RRas_bdg	e5dcxF1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
E	Piezo_RRas_bdg	e5dcxE1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
D	Piezo_RRas_bdg	e5dcxD1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
C	Piezo_RRas_bdg	e5dcxC1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
B	Piezo_RRas_bdg	e5dcxB1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)
A	Piezo_RRas_bdg	e5dcxA1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Piezo_RRas_bdg	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	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)
I	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)
G	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)
E	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)
C	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)
A	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	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 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
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	IPR049901	NS1 nuclease, NS1-Nuc domain, Parvovirus	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 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.