Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4JKR

Crystal Structure of E. coli RNA Polymerase in complex with ppGpp

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0006351	biological_process	DNA-templated transcription
A	0046983	molecular_function	protein dimerization activity
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed RNA polymerase activity
B	0006351	biological_process	DNA-templated transcription
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 RNA polymerase activity
C	0006351	biological_process	DNA-templated transcription
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0032549	molecular_function	ribonucleoside binding
C	0034062	molecular_function	5'-3' RNA polymerase activity
D	0003677	molecular_function	DNA binding
D	0003899	molecular_function	DNA-directed RNA polymerase activity
D	0006351	biological_process	DNA-templated transcription
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed RNA polymerase activity
E	0006351	biological_process	DNA-templated transcription
F	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
F	0000976	molecular_function	transcription cis-regulatory region binding
F	0003677	molecular_function	DNA binding
F	0003700	molecular_function	DNA-binding transcription factor activity
F	0003899	molecular_function	DNA-directed RNA polymerase 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	0003677	molecular_function	DNA binding
G	0003899	molecular_function	DNA-directed RNA polymerase activity
G	0006351	biological_process	DNA-templated transcription
G	0046983	molecular_function	protein dimerization activity
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed RNA polymerase activity
H	0006351	biological_process	DNA-templated transcription
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 RNA polymerase activity
I	0006351	biological_process	DNA-templated transcription
I	0016740	molecular_function	transferase activity
I	0016779	molecular_function	nucleotidyltransferase activity
I	0032549	molecular_function	ribonucleoside binding
I	0034062	molecular_function	5'-3' RNA polymerase activity
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed RNA polymerase activity
J	0006351	biological_process	DNA-templated transcription
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed RNA polymerase activity
K	0006351	biological_process	DNA-templated transcription
L	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
L	0000976	molecular_function	transcription cis-regulatory region binding
L	0003677	molecular_function	DNA binding
L	0003700	molecular_function	DNA-binding transcription factor activity
L	0003899	molecular_function	DNA-directed RNA polymerase 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	2
Details	BINDING SITE FOR RESIDUE SR A 401

Chain	Residue
A	ASP15
A	ILE16

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SR C 1401

Chain	Residue
C	GLU813
D	ALA459

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SR C 1402

Chain	Residue
C	VAL24

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE G4P D 2001

Chain	Residue
E	ARG3
E	VAL4
E	ARG52
D	ARG362
D	LYS615
D	ILE619
D	ASP622

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN D 2002

Chain	Residue
D	CYS70
D	CYS72
D	CYS88

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 2003

Chain	Residue
D	CYS814
D	SER887
D	CYS888
D	CYS895
D	CYS898

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SR D 2004

Chain	Residue
D	ASP460
D	ASP464

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SR F 701

Chain	Residue
F	ASP581

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SR I 1401

Chain	Residue
I	GLU813

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN J 1501

Chain	Residue
J	CYS70
J	LEU71
J	CYS72
J	CYS85
J	CYS88

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN J 1502

Chain	Residue
J	CYS814
J	CYS888
J	THR890
J	CYS895
J	CYS898

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SR J 1503

Chain	Residue
J	ASP460
J	ASP464

site_id	BC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE G4P K 101

Chain	Residue
J	ARG362
J	LYS615
J	ILE619
J	ASP622
K	ALA2
K	ARG3
K	VAL4
K	THR5
K	GLU42
K	ARG52

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_FI9
Number of Residues	38
Details	DNA binding: {"description":"H-T-H motif","evidences":[{"source":"HAMAP-Rule","id":"MF_00963","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	140
Details	Region: {"description":"Sigma-70 factor domain-2"}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	152
Details	Region: {"description":"Sigma-70 factor domain-3"}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	106
Details	Region: {"description":"Sigma-70 factor domain-4"}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	30
Details	Region: {"description":"Interaction with anti-sigma factors"}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	6
Details	Motif: {"description":"Interaction with polymerase core subunit RpoC"}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Site: {"description":"Interaction with anti-sigma factors"}

Chain

Residue

Details

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