3K5L | pdb_00003k5l

Crystal structure of E.coli Pol II-abasic DNA-dATP Lt(0, 3) ternary complex

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	d3k5la1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d3k5la2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d3k5la3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribonuclease H-like	8039907	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8039908	3001272	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	PRK05762_1st	e3k5lA5	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PRK05762_1st	ECOD (1.6)
A	DNA_pol_B_2nd_1	e3k5lA4	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: DNA_pol_B_2nd_1	ECOD (1.6)
A	DNA_pol_B_1st_1	e3k5lA6	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: DNA_pol_B_1st_1	ECOD (1.6)
A	PRK05762_2nd	e3k5lA3	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: PRK05762_2nd	ECOD (1.6)
A	DNA_pol_B_exo1_3rd	e3k5lA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_B_exo1_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.590	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	DNA polymerase B, N domain, beta-barrel	CATH (4.3.0)
A	3.30.70.2250	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	B family DNA polymerase, N domain, alpha/beta motif	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	6.10.140.1130	Special	Helix non-globular	Helix Hairpins		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)
A	1.10.132.60	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21474	DNA polymerase II, N-terminal (DNApolII_N)	DNA polymerase II, N-terminal	This is the N-terminal domain of bacterial DNA polymerase II. This entry represents the OB fold [1].	Domain
A	PF22587	DNA polymerase II, insertion domain (DNApolII_insertion)	DNA polymerase II, insertion domain	This is the insertion domain found in DNA polymerase II from E. coli, a member of family B of DNA polymerases [1].	Domain
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
A	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA polymerase II	DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA-directed DNA polymerase activity DNA polymerase activity DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus response to stimulus DNA-templated DNA replication maintenance of fidelity DNA replication proofreading cellular response to stress nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus response to stimulus DNA-templated DNA replication maintenance of fidelity DNA replication proofreading cellular response to stress DNA damage response response to stress DNA repair SOS response	-
B [auth T]	DNA (5'-D(TPAPTP(3DR)PGPTPAPCPGPCPTPAPGPGPCPAPCPA)-3')	-	-	-
C [auth P]	DNA (5'-D(GPTPGPCPCPTPAPGPCPGPTPAP*(DOC))-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A	IPR055208	DNA polymerase II, insertion domain	Domain
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR050240	DNA polymerase type-B	Family
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
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

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.