Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4YFK

Escherichia coli RNA polymerase in complex with squaramide compound 8.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0016779	molecular_function	nucleotidyltransferase activity
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0046983	molecular_function	protein dimerization activity
B	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0016779	molecular_function	nucleotidyltransferase activity
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0046983	molecular_function	protein dimerization activity
C	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0016779	molecular_function	nucleotidyltransferase activity
C	0032549	molecular_function	ribonucleoside binding
C	0034062	molecular_function	5'-3' RNA polymerase activity
D	0000287	molecular_function	magnesium ion binding
D	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0008270	molecular_function	zinc ion binding
D	0016779	molecular_function	nucleotidyltransferase activity
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0046872	molecular_function	metal ion binding
E	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0016779	molecular_function	nucleotidyltransferase activity
E	0034062	molecular_function	5'-3' RNA polymerase activity
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	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	0016779	molecular_function	nucleotidyltransferase activity
G	0034062	molecular_function	5'-3' RNA polymerase activity
G	0046983	molecular_function	protein dimerization activity
H	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0016779	molecular_function	nucleotidyltransferase activity
H	0034062	molecular_function	5'-3' RNA polymerase activity
H	0046983	molecular_function	protein dimerization activity
I	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0016779	molecular_function	nucleotidyltransferase activity
I	0032549	molecular_function	ribonucleoside binding
I	0034062	molecular_function	5'-3' RNA polymerase activity
J	0000287	molecular_function	magnesium ion binding
J	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0008270	molecular_function	zinc ion binding
J	0016779	molecular_function	nucleotidyltransferase activity
J	0034062	molecular_function	5'-3' RNA polymerase activity
J	0046872	molecular_function	metal ion binding
K	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0016779	molecular_function	nucleotidyltransferase activity
K	0034062	molecular_function	5'-3' RNA polymerase activity
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 C 1401

Chain	Residue
C	GLU813
D	ALA459
D	ASP460

site_id	AC2
Number of Residues	2
Details	binding site for residue MG D 2001

Chain	Residue
D	ASP462
D	ASP464

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN D 2002

Chain	Residue
D	CYS70
D	CYS72
D	CYS85
D	CYS88

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN D 2003

Chain	Residue
D	CYS814
D	CYS888
D	CYS895
D	CYS898

site_id	AC5
Number of Residues	11
Details	binding site for residue 4C6 D 2004

Chain	Residue
C	LEU1326
C	ILE1330
D	ILE331
D	LEU342
D	GLY344
D	LYS345
D	ILE1320
D	ALA1323
D	LEU1332
D	VAL1351
D	ILE1352

site_id	AC6
Number of Residues	4
Details	binding site for residue MG I 1401

Chain	Residue
I	GLU813
J	CYS454
J	ALA459
J	ASP460

site_id	AC7
Number of Residues	2
Details	binding site for residue MG J 2001

Chain	Residue
J	ASP462
J	ASP464

site_id	AC8
Number of Residues	3
Details	binding site for residue ZN J 2002

Chain	Residue
J	CYS70
J	CYS72
J	CYS85

site_id	AC9
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	AD1
Number of Residues	11
Details	binding site for residue 4C6 J 2004

Chain	Residue
I	PHE1270
I	GLU1272
I	LEU1326
J	ILE331
J	LEU342
J	LEU343
J	GLY344
J	LYS345
J	ALA1323
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)