1TKD | pdb_00001tkd

T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site

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 [auth B]	d1tkdb_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Thioltransferase	Thioredoxin	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth A]	d1tkda1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of T7 DNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
C [auth A]	d1tkda2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	T7 phage DNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	Thioredoxin-like	8044359	3000031	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8040253	3000143	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8040254	3001272	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8040254	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)
D [auth B]		e1tkdB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Thioredoxin	F:	ECOD (20:10:01)
C [auth A]		e1tkdA1	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: Ribonuclease_3	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
C [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C [auth A]	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
C [auth A]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth B]	PF00085	Thioredoxin (Thioredoxin)	Thioredoxin	Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.	Domain
C [auth A]	PF00476	DNA polymerase family A (DNA_pol_A)	DNA polymerase family A		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P]	DNA (5'-D(CPGPAPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPAP(DOC))-3')	-	-	-
D [auth B]	Thioredoxin 1	enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity catalytic activity	cell redox homeostasis cellular homeostasis homeostatic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
C [auth A]	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 DNA exonuclease activity DNA nuclease activity 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 metabolic process cellular 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 metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA synthesis involved in DNA replication DNA replication DNA-templated DNA replication cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair	-
B [auth T]	DNA (5'-D(CPCPCPAP(8OG)PTPGPGPCPAPCPTPGPGPCPCPGPTPCPGPTPTPTPTPCPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth B]	IPR017937	Thioredoxin, conserved site	Conserved Site
D [auth B]	IPR013766	Thioredoxin domain	Domain
D [auth B]	IPR005746	Thioredoxin	Family
D [auth B]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
C [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth A]	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
C [auth A]	IPR034699	DNA-directed DNA polymerase T7	Family
C [auth A]	IPR002298	DNA polymerase A	Family
C [auth A]	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
C [auth A]	IPR012337	Ribonuclease H-like 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.