Annotations: 6KNB

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	PCNA_C	e6knbE1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
E	PCNA_N_1	e6knbE2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N_1	ECOD (1.6)
D	PCNA_C	e6knbD2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
D	PCNA_N_1	e6knbD1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N_1	ECOD (1.6)
C	PCNA_C	e6knbC1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
C	PCNA_N_1	e6knbC2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N_1	ECOD (1.6)
A	tRNA_anti-codon	e6knbA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_anti-codon	ECOD (1.6)
A	DNA_pol_E_B	e6knbA2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: DNA_pol_E_B	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF24846	DNA polymerase II large subunit DP2, catalytic domain (PolC_DP2_cat)	DNA polymerase II large subunit DP2, catalytic domain	This entry represents the catalytic domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain is found C-terminal to Pfam:PF24844 and shows a six-stranded double-psi beta-barrel ...	This entry represents the catalytic domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain is found C-terminal to Pfam:PF24844 and shows a six-stranded double-psi beta-barrel (DPBB) [1].	Domain
B	PF03833	DNA polymerase II large subunit DP2, N-terminal (PolC_DP2_N)	DNA polymerase II large subunit DP2, N-terminal	This entry represents the N-terminal domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain shows an alpha beta configuration [1].	Domain
B	PF24844	DNA polymerase II large subunit DP2, central domain (PolC_DP2_central)	DNA polymerase II large subunit DP2, central domain	This entry represents the central domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain, which is found C-terminal to Pfam:PF03833, shows an alpha-beta configuration [1].	Domain
C, D, E	PF02747	Proliferating cell nuclear antigen, C-terminal domain (PCNA_C)	Proliferating cell nuclear antigen, C-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
C, D, E	PF00705	Proliferating cell nuclear antigen, N-terminal domain (PCNA_N)	Proliferating cell nuclear antigen, N-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
A	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	DNA polymerase D DP2 (DNA polymerase II large) subunit	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 DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity 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 DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity endonuclease activity	catabolic 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 catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process intein-mediated protein splicing gene expression catabolic 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 catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process intein-mediated protein splicing gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process protein splicing DNA recombination intron homing DNA-templated DNA replication DNA replication	-
C, D, E	DNA polymerase sliding clamp 1	DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding	DNA-templated DNA replication primary metabolic process DNA metabolic process leading strand elongation nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process regulation of biological process regulation of cellular process DNA-templated DNA replication primary metabolic process DNA metabolic process leading strand elongation nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process	-
F	pri25DNA	-	-	-
G	temp35DNA	-	-	-
A	DNA polymerase II small subunit	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 DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity 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 DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	catabolic 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 catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation catabolic 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 catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation DNA replication DNA strand elongation involved in DNA replication	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR016033	DNA polymerase II large subunit DP2, N-terminal	Domain
B	IPR036844	Hint domain superfamily	Homologous Superfamily
B	IPR030934	Intein C-terminal splicing region	Conserved Site
B	IPR006142	Intein	Domain
B	IPR004042	Intein DOD homing endonuclease, central region	Domain
B	IPR027434	Homing endonuclease	Homologous Superfamily
B	IPR006141	Intein N-terminal splicing region	PTM
B	IPR004860	Homing endonuclease, LAGLIDADG domain	Domain
B	IPR056171	DNA polymerase II large subunit DP2, central domain	Domain
B	IPR056172	DNA polymerase II large subunit DP2, catalytic domain	Domain
B	IPR003587	Hint domain N-terminal	Domain
B	IPR004475	DNA polymerase II large subunit DP2	Family
B	IPR003586	Hint domain C-terminal	Domain
C, D, E	IPR046938	DNA clamp superfamily	Homologous Superfamily
C, D, E	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
C, D, E	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
C, D, E	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
C, D, E	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
A	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
A	IPR054750	DNA polymerase II small subunit, N-terminal domain	Domain
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR011149	DNA polymerase II small subunit, archaeal	Family
A	IPR024826	DNA polymerase delta/II small subunit family	Family
A	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily