1VK0 | pdb_00001vk0

X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d1vk0a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Hypothetical protein AT5G06450	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d1vk0a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d1vk0b1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Hypothetical protein AT5G06450	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d1vk0b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d1vk0c1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Hypothetical protein AT5G06450	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d1vk0c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d1vk0d1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Hypothetical protein AT5G06450	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d1vk0d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d1vk0e1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Hypothetical protein AT5G06450	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d1vk0e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d1vk0f1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Hypothetical protein AT5G06450	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d1vk0f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DnaQ-like 3'-5' exonuclease	8023610	4000547	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8035990	3000143	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8035990	3000143	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8035990	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8035990	3000143	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribonuclease H-like	8035990	3000143	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribonuclease H-like	8035990	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	DNA_pol_A_exo1	e1vk0A1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1	ECOD (1.6)
B	DNA_pol_A_exo1	e1vk0B1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1	ECOD (1.6)
C	DNA_pol_A_exo1	e1vk0C1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1	ECOD (1.6)
D	DNA_pol_A_exo1	e1vk0D1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1	ECOD (1.6)
E	DNA_pol_A_exo1	e1vk0E1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1	ECOD (1.6)
F	DNA_pol_A_exo1	e1vk0F1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

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	hypothetical protein	binding nucleic acid binding RISC complex binding ribonucleoprotein complex binding protein-containing complex binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exoribonuclease II activity binding nucleic acid binding RISC complex binding ribonucleoprotein complex binding protein-containing complex binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exoribonuclease II activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process positive regulation of biological process RNA metabolic process positive regulation of miRNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process primary metabolic process nucleic acid metabolic process positive regulation of RNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle plant-type vacuole vacuole intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR051132	3'-5' Exonuclease domain-containing protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR012337	Ribonuclease H-like superfamily	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.