1YNN | pdb_00001ynn

Taq RNA polymerase-rifampicin complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
F [auth K]	d1ynnk1	All alpha proteins	RPB6/omega subunit-like	RPB6/omega subunit-like	RNA polymerase omega subunit	RNA polymerase omega subunit	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
D	d1ynnd1	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta-prime	RNA-polymerase beta-prime	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
C	d1ynnc1	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta	RNA-polymerase beta	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
B	d1ynnb1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
B	d1ynnb2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
A	d1ynna1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
A	d1ynna2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth K]	SCOP2B Superfamily	RPB6/omega subunit-like	8034762	3000189	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032539	3001330	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032536	3001330	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032536	3001330	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8034760	3001500	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8034760	3001500	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth K]	e1ynnK1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: IMS_HHH	F:	ECOD (20:10:01)
E [auth J]	e1ynnJ1	A: Ribosomal protein L31e-like	X: Reductive activator for corrinoid/iron-sulfur protein second domain	H: Reductive activator for corrinoid/iron-sulfur protein second domain	T: RACo_linker	F:	ECOD (20:10:01)
D	e1ynnD1	A: Lipocalins/Streptavidin	X: Enterocin 7A and 7B	H: Enterocin 7A and 7B	T: SHQ1-like_CS	F:	ECOD (20:10:01)
D	e1ynnD9	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: C1-set	F:	ECOD (20:10:01)
C	e1ynnC4	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: CBAH	F:	ECOD (20:10:01)
C	e1ynnC6	A: UBC-like	X: UBC-like	H: Concanavalin A-like lectins/glucanases	T: Pyr_redox_2	F:	ECOD (20:10:01)
C	e1ynnC8	A: Four-helical up-and-down bundle	X: Thymidylate synthase/dCMP hydroxymethylase	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylat_synt	F:	ECOD (20:10:01)
B	e1ynnB1	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: DUF3197	F:	ECOD (20:10:01)
B	e1ynnB2	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: CBAH	F:	ECOD (20:10:01)
A	e1ynnA1	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: DUF3197	F:	ECOD (20:10:01)
A	e1ynnA2	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: CBAH	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth K]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)
E [auth J]	1.10.1790.20	Mainly Alpha	Orthogonal Bundle	PTS-regulatory domain, PRD		CATH (4.3.0)
E [auth J]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
E [auth J]	1.10.150.390	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
D	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
D	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
D	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
C	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
C	3.90.1100.10	Alpha Beta	Alpha-Beta Complex	Rna Polymerase Beta Subunit	Chain: C,domain 2	CATH (4.3.0)
C	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
C	2.30.150.10	Mainly Beta	Roll	Rna Polymerase Beta Subunit	Chain: C, domain 4	CATH (4.3.0)
C	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
C	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
B	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
A	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth K]	DNA-directed RNA polymerase omega chain	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
D, E [auth J]	DNA-directed RNA polymerase beta' chain	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups transition metal ion binding zinc ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
C	DNA-directed RNA polymerase beta chain	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
A, B	DNA-directed RNA polymerase alpha chain	DNA binding binding nucleic acid binding protein binding protein dimerization activity DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth K]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
F [auth K]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
F [auth K]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
D, E [auth J]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D, E [auth J]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D, E [auth J]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D, E [auth J]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
D, E [auth J]	IPR048566	DNA-directed RNA polymerase subunit beta', hybrid domain	Domain
D, E [auth J]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D, E [auth J]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D, E [auth J]	IPR000722	RNA polymerase, alpha subunit	Domain
D, E [auth J]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D, E [auth J]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D, E [auth J]	IPR006592	RNA polymerase, N-terminal	Domain
D, E [auth J]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
C	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C	IPR007641	RNA polymerase Rpb2, domain 7	Domain
A, B	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A, B	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily