3I8D | pdb_00003i8d

The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

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)
C	d3i8dc_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Ribonuclease H	BH0863-like Ribonuclease H	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)
A	d3i8da_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Ribonuclease H	BH0863-like Ribonuclease H	(Halalkalibacterium halodurans ) [TaxId: 86665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Ribonuclease H-like	8035526	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8035526	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)
C	HTH_3	e3i8dC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3	ECOD (v294.1)
A	HTH_3	e3i8dA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	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
B, D	5'-D(CPGPCPGPAPAPTP(DFT)PCPGPCPG)-3'	-	-	-
A, C	Ribonuclease H	binding nucleic acid binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity cation binding binding nucleic acid binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity cation binding ion binding metal ion binding small molecule binding	DNA replication, removal of RNA primer catabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA replication nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA replication, removal of RNA primer catabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA replication nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, C	IPR037056	Ribonuclease H1, N-terminal domain superfamily	Homologous Superfamily
A, C	IPR002156	Ribonuclease H domain	Domain
A, C	IPR050092	Ribonuclease H	Family
A, C	IPR011320	Ribonuclease H1, N-terminal	Domain
A, C	IPR009027	Large ribosomal subunit protein bL9/RNase H1, N-terminal	Homologous Superfamily
A, C	IPR017290	Ribonuclease H, Bacteroides-type	Family
A, C	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.