2DTU

Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog

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)
I [auth A]	d2dtua1	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	(Escherichia phage RB69 ) [TaxId: 12353 ],	SCOPe (2.08)
I [auth A]	d2dtua2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	Family B DNA polymerase	(Escherichia phage RB69 ) [TaxId: 12353 ],	SCOPe (2.08)
J [auth B]	d2dtub1	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	(Escherichia phage RB69 ) [TaxId: 12353 ],	SCOPe (2.08)
J [auth B]	d2dtub2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	Family B DNA polymerase	(Escherichia phage RB69 ) [TaxId: 12353 ],	SCOPe (2.08)
K [auth C]	d2dtuc1	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	(Escherichia phage RB69 ) [TaxId: 12353 ],	SCOPe (2.08)
K [auth C]	d2dtuc2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	Family B DNA polymerase	(Escherichia phage RB69 ) [TaxId: 12353 ],	SCOPe (2.08)
L [auth D]	d2dtud1	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	(Escherichia phage RB69 ) [TaxId: 12353 ],	SCOPe (2.08)
L [auth D]	d2dtud2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	Family B DNA polymerase	(Escherichia phage RB69 ) [TaxId: 12353 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	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)
I [auth A]	43_2nd	e2dtuA5	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: 43_2nd	ECOD (1.6)
I [auth A]	43_1st	e2dtuA6	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: 43_1st	ECOD (1.6)
I [auth A]	DNA_pol_B_1st	e2dtuA7	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	ECOD (1.6)
I [auth A]	DNA_pol_B_exo1_3rd	e2dtuA4	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)
J [auth B]	43_2nd	e2dtuB5	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: 43_2nd	ECOD (1.6)
J [auth B]	43_1st	e2dtuB6	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: 43_1st	ECOD (1.6)
J [auth B]	DNA_pol_B_1st	e2dtuB7	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	ECOD (1.6)
J [auth B]	DNA_pol_B_exo1_3rd	e2dtuB4	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)
K [auth C]	43_2nd	e2dtuC6	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: 43_2nd	ECOD (1.6)
K [auth C]	43_1st	e2dtuC7	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: 43_1st	ECOD (1.6)
K [auth C]	DNA_pol_B_1st	e2dtuC5	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	ECOD (1.6)
K [auth C]	DNA_pol_B_exo1_3rd	e2dtuC4	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)
L [auth D]	43_2nd	e2dtuD6	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: 43_2nd	ECOD (1.6)
L [auth D]	43_1st	e2dtuD7	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: 43_1st	ECOD (1.6)
L [auth D]	DNA_pol_B_1st	e2dtuD5	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	ECOD (1.6)
L [auth D]	DNA_pol_B_exo1_3rd	e2dtuD4	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)
I [auth A]	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
I [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
I [auth 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)
I [auth A]	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
I [auth A]	1.20.1280.300	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
I [auth A]	3.40.1820.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease H-like motif	DnaQ-like 3'-5' exonuclease	CATH (4.3.0)
J [auth B]	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
J [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
J [auth B]	3.90.1600.10	Alpha Beta	Alpha-Beta Complex	Palm domain of DNA polymerase	B family DNA polymerase, palm domain	CATH (4.3.0)
J [auth B]	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
J [auth B]	1.20.1280.300	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
J [auth B]	3.40.1820.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease H-like motif	DnaQ-like 3'-5' exonuclease	CATH (4.3.0)
K [auth C]	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
K [auth C]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
K [auth C]	3.90.1600.10	Alpha Beta	Alpha-Beta Complex	Palm domain of DNA polymerase	B family DNA polymerase, palm domain	CATH (4.3.0)
K [auth C]	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
K [auth C]	1.20.1280.300	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
K [auth C]	3.40.1820.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease H-like motif	DnaQ-like 3'-5' exonuclease	CATH (4.3.0)
L [auth D]	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
L [auth D]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
L [auth D]	3.90.1600.10	Alpha Beta	Alpha-Beta Complex	Palm domain of DNA polymerase	B family DNA polymerase, palm domain	CATH (4.3.0)
L [auth D]	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
L [auth D]	1.20.1280.300	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
L [auth D]	3.40.1820.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease H-like motif	DnaQ-like 3'-5' exonuclease	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth A], J [auth B], K [auth C], L [auth D]	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
I [auth A], J [auth B], K [auth C], L [auth D]	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 [auth E], C [auth G], E [auth I], G [auth K]	5'-D(CPGP(3DR)PCPTPTPAPTPGPAPCPAPGPCPCPGPCPG)-3'	-	-	-
B [auth F], D [auth H], F [auth J], H [auth L]	5'-D(GPCPGPGPCPTPGPTPCPAPTPAPAPGP*A)-3'	-	-	-
I [auth A], J [auth B], K [auth C], L [auth D]	DNA polymerase	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 organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 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 organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process viral life cycle nucleic acid biosynthetic process organic substance biosynthetic process viral process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process viral life cycle nucleic acid biosynthetic process organic substance biosynthetic process viral process bidirectional double-stranded viral DNA replication cellular metabolic process viral DNA genome replication nucleobase-containing compound biosynthetic process macromolecule biosynthetic process biosynthetic process viral genome replication organic cyclic compound biosynthetic process cellular process DNA biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A], J [auth B], K [auth C], L [auth D]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR034749	DNA-directed DNA polymerase T4 type	Family
I [auth A], J [auth B], K [auth C], L [auth D]	IPR006172	DNA-directed DNA polymerase, family B	Family
I [auth A], J [auth B], K [auth C], L [auth D]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
I [auth A], J [auth B], K [auth C], L [auth D]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily