Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4YFN

Escherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0001054	molecular_function	RNA polymerase I activity
A	0001055	molecular_function	RNA polymerase II activity
A	0001056	molecular_function	RNA polymerase III activity
A	0001057	molecular_function	RNA polymerase IV activity
A	0001058	molecular_function	RNA polymerase V activity
A	0001059	biological_process	transcription by RNA polymerase IV
A	0001060	biological_process	transcription by RNA polymerase V
A	0001066	molecular_function	plastid single subunit type RNA polymerase activity
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0005737	cellular_component	cytoplasm
A	0006351	biological_process	DNA-templated transcription
A	0006360	biological_process	transcription by RNA polymerase I
A	0006366	biological_process	transcription by RNA polymerase II
A	0006383	biological_process	transcription by RNA polymerase III
A	0016779	molecular_function	nucleotidyltransferase activity
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0042793	biological_process	plastid transcription
A	0046983	molecular_function	protein dimerization activity
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0001054	molecular_function	RNA polymerase I activity
B	0001055	molecular_function	RNA polymerase II activity
B	0001056	molecular_function	RNA polymerase III activity
B	0001057	molecular_function	RNA polymerase IV activity
B	0001058	molecular_function	RNA polymerase V activity
B	0001059	biological_process	transcription by RNA polymerase IV
B	0001060	biological_process	transcription by RNA polymerase V
B	0001066	molecular_function	plastid single subunit type RNA polymerase activity
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0005737	cellular_component	cytoplasm
B	0006351	biological_process	DNA-templated transcription
B	0006360	biological_process	transcription by RNA polymerase I
B	0006366	biological_process	transcription by RNA polymerase II
B	0006383	biological_process	transcription by RNA polymerase III
B	0016779	molecular_function	nucleotidyltransferase activity
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0042793	biological_process	plastid transcription
B	0046983	molecular_function	protein dimerization activity
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0001054	molecular_function	RNA polymerase I activity
C	0001055	molecular_function	RNA polymerase II activity
C	0001056	molecular_function	RNA polymerase III activity
C	0001057	molecular_function	RNA polymerase IV activity
C	0001058	molecular_function	RNA polymerase V activity
C	0001059	biological_process	transcription by RNA polymerase IV
C	0001060	biological_process	transcription by RNA polymerase V
C	0001066	molecular_function	plastid single subunit type RNA polymerase activity
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
C	0006351	biological_process	DNA-templated transcription
C	0006360	biological_process	transcription by RNA polymerase I
C	0006366	biological_process	transcription by RNA polymerase II
C	0006383	biological_process	transcription by RNA polymerase III
C	0016779	molecular_function	nucleotidyltransferase activity
C	0032549	molecular_function	ribonucleoside binding
C	0034062	molecular_function	5'-3' RNA polymerase activity
C	0042793	biological_process	plastid transcription
D	0000287	molecular_function	magnesium ion binding
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0001054	molecular_function	RNA polymerase I activity
D	0001055	molecular_function	RNA polymerase II activity
D	0001056	molecular_function	RNA polymerase III activity
D	0001057	molecular_function	RNA polymerase IV activity
D	0001058	molecular_function	RNA polymerase V activity
D	0001059	biological_process	transcription by RNA polymerase IV
D	0001060	biological_process	transcription by RNA polymerase V
D	0001066	molecular_function	plastid single subunit type RNA polymerase activity
D	0003677	molecular_function	DNA binding
D	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
D	0006351	biological_process	DNA-templated transcription
D	0006360	biological_process	transcription by RNA polymerase I
D	0006366	biological_process	transcription by RNA polymerase II
D	0006383	biological_process	transcription by RNA polymerase III
D	0008270	molecular_function	zinc ion binding
D	0016779	molecular_function	nucleotidyltransferase activity
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0042793	biological_process	plastid transcription
D	0046872	molecular_function	metal ion binding
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0001054	molecular_function	RNA polymerase I activity
E	0001055	molecular_function	RNA polymerase II activity
E	0001056	molecular_function	RNA polymerase III activity
E	0001057	molecular_function	RNA polymerase IV activity
E	0001058	molecular_function	RNA polymerase V activity
E	0001059	biological_process	transcription by RNA polymerase IV
E	0001060	biological_process	transcription by RNA polymerase V
E	0001066	molecular_function	plastid single subunit type RNA polymerase activity
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
E	0006351	biological_process	DNA-templated transcription
E	0006360	biological_process	transcription by RNA polymerase I
E	0006366	biological_process	transcription by RNA polymerase II
E	0006383	biological_process	transcription by RNA polymerase III
E	0016779	molecular_function	nucleotidyltransferase activity
E	0034062	molecular_function	5'-3' RNA polymerase activity
E	0042793	biological_process	plastid transcription
F	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
F	0003677	molecular_function	DNA binding
F	0003700	molecular_function	DNA-binding transcription factor activity
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006351	biological_process	DNA-templated transcription
F	0006352	biological_process	DNA-templated transcription initiation
F	0006355	biological_process	regulation of DNA-templated transcription
F	0009408	biological_process	response to heat
F	0010468	biological_process	regulation of gene expression
F	0016987	molecular_function	sigma factor activity
F	0045892	biological_process	negative regulation of DNA-templated transcription
F	1903865	cellular_component	sigma factor antagonist complex
F	2000142	biological_process	regulation of DNA-templated transcription initiation
G	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0001054	molecular_function	RNA polymerase I activity
G	0001055	molecular_function	RNA polymerase II activity
G	0001056	molecular_function	RNA polymerase III activity
G	0001057	molecular_function	RNA polymerase IV activity
G	0001058	molecular_function	RNA polymerase V activity
G	0001059	biological_process	transcription by RNA polymerase IV
G	0001060	biological_process	transcription by RNA polymerase V
G	0001066	molecular_function	plastid single subunit type RNA polymerase activity
G	0003677	molecular_function	DNA binding
G	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
G	0005737	cellular_component	cytoplasm
G	0006351	biological_process	DNA-templated transcription
G	0006360	biological_process	transcription by RNA polymerase I
G	0006366	biological_process	transcription by RNA polymerase II
G	0006383	biological_process	transcription by RNA polymerase III
G	0016779	molecular_function	nucleotidyltransferase activity
G	0034062	molecular_function	5'-3' RNA polymerase activity
G	0042793	biological_process	plastid transcription
G	0046983	molecular_function	protein dimerization activity
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0001054	molecular_function	RNA polymerase I activity
H	0001055	molecular_function	RNA polymerase II activity
H	0001056	molecular_function	RNA polymerase III activity
H	0001057	molecular_function	RNA polymerase IV activity
H	0001058	molecular_function	RNA polymerase V activity
H	0001059	biological_process	transcription by RNA polymerase IV
H	0001060	biological_process	transcription by RNA polymerase V
H	0001066	molecular_function	plastid single subunit type RNA polymerase activity
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
H	0005737	cellular_component	cytoplasm
H	0006351	biological_process	DNA-templated transcription
H	0006360	biological_process	transcription by RNA polymerase I
H	0006366	biological_process	transcription by RNA polymerase II
H	0006383	biological_process	transcription by RNA polymerase III
H	0016779	molecular_function	nucleotidyltransferase activity
H	0034062	molecular_function	5'-3' RNA polymerase activity
H	0042793	biological_process	plastid transcription
H	0046983	molecular_function	protein dimerization activity
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0001054	molecular_function	RNA polymerase I activity
I	0001055	molecular_function	RNA polymerase II activity
I	0001056	molecular_function	RNA polymerase III activity
I	0001057	molecular_function	RNA polymerase IV activity
I	0001058	molecular_function	RNA polymerase V activity
I	0001059	biological_process	transcription by RNA polymerase IV
I	0001060	biological_process	transcription by RNA polymerase V
I	0001066	molecular_function	plastid single subunit type RNA polymerase activity
I	0003677	molecular_function	DNA binding
I	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
I	0006351	biological_process	DNA-templated transcription
I	0006360	biological_process	transcription by RNA polymerase I
I	0006366	biological_process	transcription by RNA polymerase II
I	0006383	biological_process	transcription by RNA polymerase III
I	0016779	molecular_function	nucleotidyltransferase activity
I	0032549	molecular_function	ribonucleoside binding
I	0034062	molecular_function	5'-3' RNA polymerase activity
I	0042793	biological_process	plastid transcription
J	0000287	molecular_function	magnesium ion binding
J	0000428	cellular_component	DNA-directed RNA polymerase complex
J	0001054	molecular_function	RNA polymerase I activity
J	0001055	molecular_function	RNA polymerase II activity
J	0001056	molecular_function	RNA polymerase III activity
J	0001057	molecular_function	RNA polymerase IV activity
J	0001058	molecular_function	RNA polymerase V activity
J	0001059	biological_process	transcription by RNA polymerase IV
J	0001060	biological_process	transcription by RNA polymerase V
J	0001066	molecular_function	plastid single subunit type RNA polymerase activity
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
J	0006351	biological_process	DNA-templated transcription
J	0006360	biological_process	transcription by RNA polymerase I
J	0006366	biological_process	transcription by RNA polymerase II
J	0006383	biological_process	transcription by RNA polymerase III
J	0008270	molecular_function	zinc ion binding
J	0016779	molecular_function	nucleotidyltransferase activity
J	0034062	molecular_function	5'-3' RNA polymerase activity
J	0042793	biological_process	plastid transcription
J	0046872	molecular_function	metal ion binding
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0001054	molecular_function	RNA polymerase I activity
K	0001055	molecular_function	RNA polymerase II activity
K	0001056	molecular_function	RNA polymerase III activity
K	0001057	molecular_function	RNA polymerase IV activity
K	0001058	molecular_function	RNA polymerase V activity
K	0001059	biological_process	transcription by RNA polymerase IV
K	0001060	biological_process	transcription by RNA polymerase V
K	0001066	molecular_function	plastid single subunit type RNA polymerase activity
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
K	0006351	biological_process	DNA-templated transcription
K	0006360	biological_process	transcription by RNA polymerase I
K	0006366	biological_process	transcription by RNA polymerase II
K	0006383	biological_process	transcription by RNA polymerase III
K	0016779	molecular_function	nucleotidyltransferase activity
K	0034062	molecular_function	5'-3' RNA polymerase activity
K	0042793	biological_process	plastid transcription
L	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
L	0003677	molecular_function	DNA binding
L	0003700	molecular_function	DNA-binding transcription factor activity
L	0005515	molecular_function	protein binding
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0006351	biological_process	DNA-templated transcription
L	0006352	biological_process	DNA-templated transcription initiation
L	0006355	biological_process	regulation of DNA-templated transcription
L	0009408	biological_process	response to heat
L	0010468	biological_process	regulation of gene expression
L	0016987	molecular_function	sigma factor activity
L	0045892	biological_process	negative regulation of DNA-templated transcription
L	1903865	cellular_component	sigma factor antagonist complex
L	2000142	biological_process	regulation of DNA-templated transcription initiation

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue MG D 2001

Chain	Residue
D	ASP460
D	ASP462
D	ASP464

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN D 2002

Chain	Residue
D	CYS70
D	CYS72
D	CYS85
D	CYS88

site_id	AC3
Number of Residues	5
Details	binding site for residue ZN D 2003

Chain	Residue
D	CYS888
D	CYS895
D	CYS898
D	CYS814
D	ARG883

site_id	AC4
Number of Residues	10
Details	binding site for residue 4C2 D 2004

Chain	Residue
C	GLU1272
C	PHE1323
C	ILE1330
D	ILE331
D	LYS332
D	GLY344
D	PHE1319
D	ALA1323
D	VAL1351
D	ILE1352

site_id	AC5
Number of Residues	3
Details	binding site for residue MG J 2001

Chain	Residue
J	ASP460
J	ASP462
J	ASP464

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN J 2002

Chain	Residue
J	CYS70
J	CYS72
J	CYS85
J	CYS88

site_id	AC7
Number of Residues	5
Details	binding site for residue ZN J 2003

Chain	Residue
J	CYS814
J	ARG883
J	CYS888
J	CYS895
J	CYS898

site_id	AC8
Number of Residues	10
Details	binding site for residue 4C2 J 2004

Chain	Residue
I	GLU1272
I	VAL1275
I	LEU1291
I	LEU1326
J	ILE331
J	LYS332
J	LYS345
J	PHE1319
J	VAL1351
J	ILE1352

Functional Information from PROSITE/UniProt

site_id	PS00715
Number of Residues	14
Details	SIGMA70_1 Sigma-70 factors family signature 1. DLIQeGnIGLMkAV

Chain	Residue	Details
F	ASP403-VAL416

site_id	PS00716
Number of Residues	27
Details	SIGMA70_2 Sigma-70 factors family signature 2. TleEVGkqfdVTrerIrQIEakaLrkL

Chain	Residue	Details
F	THR572-LEU598

site_id	PS01166
Number of Residues	13
Details	RNA_POL_BETA RNA polymerases beta chain signature. GdKMAGrHGNKGV

Chain	Residue	Details
C	GLY1063-VAL1075

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	38
Details	DNA_BIND: H-T-H motif => ECO:0000255\|HAMAP-Rule:MF_00963

Chain	Residue	Details
F	LEU573-ALA592
D	CYS895
D	CYS898
J	CYS70
J	CYS72
J	CYS85
J	CYS88
J	ASP460
J	ASP462
J	ASP464
J	CYS814
L	LEU573-ALA592
J	CYS888
J	CYS895
J	CYS898
D	CYS85
D	CYS88
D	ASP460
D	ASP462
D	ASP464
D	CYS814
D	CYS888

site_id	SWS_FT_FI2
Number of Residues	2
Details	SITE: Interaction with anti-sigma factors

Chain	Residue	Details
F	ARG562
L	ARG562

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)