3K5M

Crystal structure of E.coli Pol II-abasic DNA-ddGTP Lt(-2, 2) 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	d3k5ma1	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	d3k5ma2	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	d3k5ma3	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)
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	PF21474	e3k5mA4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF21474	ECOD (1.6)
A	F_UNCLASSIFIED	e3k5mA3	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: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e3k5mA6	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: F_UNCLASSIFIED	ECOD (1.6)
A	PF00136	e3k5mA2	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	PF22587	e3k5mA1	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: PF22587	ECOD (1.6)
A	PF03104	e3k5mA7	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	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	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 exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 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 exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 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 organic cyclic compound binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA-templated DNA replication DNA replication organic substance metabolic process metabolic 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 nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA-templated DNA replication DNA replication organic substance metabolic process metabolic 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 cellular process DNA repair SOS response	-
B [auth T]	DNA (5'-D(APGPTPCPCPTPGP(3DR)PAPCPGPCPTPAPGPGPCPAPCPA)-3')	-	-	-
C [auth P]	DNA (5'-D(GPTPGPCPCPTPAPGPCPGPTPAP*G)-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	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	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 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.