1WNS

Crystal structure of family B DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis KOD1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d1wnsa1	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 ], (Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ], (Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
A	d1wnsa2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	Family B DNA polymerase	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ], (Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ], (Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e1wnsA12	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00136	e1wnsA1	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: PF00136	ECOD (1.6)
A	PF00136	e1wnsA11	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: PF00136	ECOD (1.6)
A	PF00136	e1wnsA9	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF00136	ECOD (1.6)
A	F_UNCLASSIFIED	e1wnsA10	A: a+b two layers	X: Alpha-beta plaits	H: Family B DNA polymerase insertion domain (From Topology)	T: Family B DNA polymerase insertion domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF03104	e1wnsA8	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF03104	ECOD (1.6)

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	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	DNA POLYMERASE	binding nucleoside phosphate binding organic cyclic compound 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 binding nucleoside phosphate binding organic cyclic compound 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 nuclease activity hydrolase activity, acting on ester bonds hydrolase activity exonuclease activity DNA binding nucleic acid binding endonuclease activity	nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic 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 organonitrogen compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic 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 organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis organic substance biosynthetic process protein processing cellular process 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	IPR006141	Intein N-terminal splicing region	PTM
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	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	IPR004042	Intein DOD homing endonuclease	Domain
A	IPR027434	Homing endonuclease	Homologous Superfamily
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR004860	Homing endonuclease, LAGLIDADG	Domain
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A	IPR003587	Hint domain N-terminal	Domain
A	IPR030934	Intein C-terminal splicing region	Domain

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.