1WN7 | pdb_00001wn7

Crystal structure of archaeal family B DNA polymerase mutant

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	d1wn7a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of family B DNA polymerases	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
A	d1wn7a2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	Family B DNA polymerase	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	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	8020778	4000547	SCOP2 (2022-06-29)
A	SCOP2 Family	Type I DNA polymerase-like	8020782	4002781	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8033158	3000143	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033162	3001272	SCOP2 (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	Stap_Strp_toxin	e1wn7A1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (develop294)
A		e1wn7A2	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
A		e1wn7A3	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
A	RNase_P_Rpp14	e1wn7A4	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
A	DUF1697	e1wn7A5	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: DUF1697	ECOD (develop294)
A	Thioredoxin	e1wn7A6	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.90.1600.10	Alpha Beta	Alpha-Beta Complex	Palm domain of DNA polymerase	B family DNA polymerase, palm domain	CATH (4.3.0)
A	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Family B DNA Polymerase	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups hydrolase activity, acting on ester bonds binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups hydrolase activity, acting on ester bonds nuclease activity hydrolase activity exonuclease activity DNA binding nucleic acid binding endonuclease activity	nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process intron homing DNA-templated DNA replication DNA replication intein-mediated protein splicing gene expression macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process intron homing DNA-templated DNA replication DNA replication intein-mediated protein splicing gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process protein splicing	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR036844	Hint domain superfamily	Homologous Superfamily
A	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A	IPR006142	Intein	Domain
A	IPR004042	Intein DOD homing endonuclease, central region	Domain
A	IPR006141	Intein N-terminal splicing region	PTM
A	IPR050240	DNA polymerase type-B	Family
A	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A	IPR003586	Hint domain C-terminal	Domain
A	IPR030934	Intein C-terminal splicing region	Conserved Site
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR041005	DNA polymerase II intein domain IV	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR027434	Homing endonuclease	Homologous Superfamily
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR004860	Homing endonuclease, LAGLIDADG domain	Domain
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A	IPR003587	Hint domain N-terminal	Domain