Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6VVV

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase

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 RNA polymerase activity
A	0005737	cellular_component	cytoplasm
A	0006351	biological_process	DNA-templated transcription
A	0016740	molecular_function	transferase activity
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 RNA polymerase activity
B	0005737	cellular_component	cytoplasm
B	0006351	biological_process	DNA-templated transcription
B	0016740	molecular_function	transferase activity
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 RNA polymerase activity
C	0005515	molecular_function	protein binding
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
C	0046677	biological_process	response to antibiotic
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 RNA polymerase activity
D	0006351	biological_process	DNA-templated transcription
D	0008270	molecular_function	zinc ion binding
D	0016740	molecular_function	transferase activity
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 RNA polymerase activity
E	0006351	biological_process	DNA-templated transcription
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0034062	molecular_function	5'-3' RNA polymerase activity
F	0003677	molecular_function	DNA binding
F	0003700	molecular_function	DNA-binding transcription factor activity
F	0005737	cellular_component	cytoplasm
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	0010468	biological_process	regulation of gene expression
F	0016987	molecular_function	sigma factor activity
F	2000142	biological_process	regulation of DNA-templated transcription initiation
J	0001000	molecular_function	bacterial-type RNA polymerase core enzyme binding
J	0006351	biological_process	DNA-templated transcription
J	0045893	biological_process	positive regulation of DNA-templated transcription
J	0046677	biological_process	response to antibiotic
T	0000428	cellular_component	DNA-directed RNA polymerase complex
T	0003677	molecular_function	DNA binding
T	0003899	molecular_function	DNA-directed RNA polymerase activity
T	0005737	cellular_component	cytoplasm
T	0006351	biological_process	DNA-templated transcription
T	0016740	molecular_function	transferase activity
T	0016779	molecular_function	nucleotidyltransferase activity
T	0034062	molecular_function	5'-3' RNA polymerase activity
T	0046983	molecular_function	protein dimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	binding site for residue SO4 D 1403

Chain	Residue
D	ARG214
D	ARG218

site_id	AC2
Number of Residues	2
Details	binding site for residue SO4 D 1404

Chain	Residue
D	ARG421
D	ARG427

site_id	AC3
Number of Residues	6
Details	binding site for residue SO4 D 1405

Chain	Residue
D	ARG1164
D	ASP882
D	VAL883
D	THR971
D	GLY972
D	ARG1160

site_id	AC4
Number of Residues	2
Details	binding site for residue SO4 D 1406

Chain	Residue
D	TYR871
D	ARG874

site_id	AC5
Number of Residues	5
Details	binding site for residue SO4 D 1407

Chain	Residue
D	ARG386
D	LYS407
D	GLU1229
D	THR1230
D	THR1231

site_id	AC6
Number of Residues	3
Details	binding site for residue SO4 D 1408

Chain	Residue
D	GLY895
D	LYS960
D	ARG1129

site_id	AC7
Number of Residues	5
Details	binding site for residue ZN D 1409

Chain	Residue
D	CYS890
D	ARG962
D	CYS967
D	CYS974
D	CYS977

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN D 1410

Chain	Residue
D	CYS60
D	CYS62
D	CYS75
D	CYS78

site_id	AC9
Number of Residues	5
Details	binding site for residue SO4 F 1201

Chain	Residue
D	VAL592
D	ALA595
D	SER628
D	ARG630
F	LYS210

site_id	AD1
Number of Residues	3
Details	binding site for residue SO4 F 1202

Chain	Residue
F	ARG190
F	ARG228
F	HIS232

site_id	AD2
Number of Residues	2
Details	binding site for residue SO4 F 1203

Chain	Residue
F	ALA254
F	PHE255

site_id	AD3
Number of Residues	6
Details	binding site for residue SO4 F 1204

Chain	Residue
F	TRP287
F	ARG290
F	GLN291
F	THR294
O	DT26
P	DA1

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
F	ASP257-VAL270

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

Chain	Residue	Details
F	THR426-LEU452

site_id	PS00867
Number of Residues	8
Details	CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LLEANLRL

Chain	Residue	Details
F	LEU233-LEU240

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

Chain	Residue	Details
C	GLY873-VAL885

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	11
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01322","evidenceCode":"ECO:0000255"},{"source":"PDB","id":"6YXU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6YYS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6Z11","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	19
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_FI3
Number of Residues	34
Details	Region: {"description":"Sigma-70 factor domain-1","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	70
Details	Region: {"description":"Sigma-70 factor domain-2","evidences":[{"source":"HAMAP-Rule","id":"MF_00963","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	76
Details	Region: {"description":"Sigma-70 factor domain-3","evidences":[{"source":"HAMAP-Rule","id":"MF_00963","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	53
Details	Region: {"description":"Sigma-70 factor domain-4","evidences":[{"source":"HAMAP-Rule","id":"MF_00963","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	3
Details	Motif: {"description":"Interaction with polymerase core subunit RpoC","evidences":[{"source":"HAMAP-Rule","id":"MF_00963","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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