3RMD | pdb_00003rmd

Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol

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)
D	d3rmdd1	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)
D	d3rmdd2	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)
C	d3rmdc1	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)
C	d3rmdc2	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)
B	d3rmdb1	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)
B	d3rmdb2	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)
A	d3rmda1	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)
A	d3rmda2	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)
D	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	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)
D	Fapy_DNA_glyco	e3rmdD5	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Fapy_DNA_glyco	ECOD (develop294)
C	FeoB_Cyto	e3rmdC4	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (develop294)
C	SidM_Rab1-act	e3rmdC5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: SidM_Rab1-act	ECOD (develop294)
B	Fapy_DNA_glyco	e3rmdB5	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Fapy_DNA_glyco	ECOD (develop294)
A	Fapy_DNA_glyco	e3rmdA5	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Fapy_DNA_glyco	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
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)
D	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
D	1.20.1280.300	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
D	3.40.1820.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease H-like motif	DnaQ-like 3'-5' exonuclease	CATH (4.3.0)
C	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
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)
C	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
C	1.20.1280.300	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
C	3.40.1820.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease H-like motif	DnaQ-like 3'-5' exonuclease	CATH (4.3.0)
B	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
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)
B	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
B	1.20.1280.300	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
B	3.40.1820.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease H-like motif	DnaQ-like 3'-5' exonuclease	CATH (4.3.0)
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)
A	1.20.1280.300	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
A	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
A, B, C, D	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
A, B, C, D	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
F, H, J, L	DNA (5'-D(GPCPGPGPCPTPGPTPCPAPTPTPCPAP*A)-3')	-	-	-
E, G, I, K	DNA (5'-D(CPGPTP(CTG)PGAPAPTPGPAPCPAPGPCPCPGPCPG)-3')	-	-	-
A, B, C, 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 nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity 3'-5' exonuclease 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 hydrolase activity, acting on ester bonds nuclease activity 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	viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication metabolic process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA replication	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A, B, C, D	IPR034749	DNA-directed DNA polymerase T4 type	Family
A, B, C, D	IPR006172	DNA-directed DNA polymerase, family B	Family
A, B, C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A, B, C, D	IPR050240	DNA polymerase type-B	Family
A, B, C, D	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A, B, C, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily