Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5VI8

Structure of a mycobacterium smegmatis transcription initiation complex with an upstream-fork promoter fragment

Replaces: 5TW1

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	0005515	molecular_function	protein binding
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
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 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	0003677	molecular_function	DNA binding
F	0003700	molecular_function	DNA-binding transcription factor activity
F	0005737	cellular_component	cytoplasm
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	0045893	biological_process	positive regulation of DNA-templated transcription
J	0046677	biological_process	response to antibiotic
T	0003677	molecular_function	DNA binding
T	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
T	0006351	biological_process	DNA-templated transcription

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue SO4 C 1201

Chain	Residue
C	ARG595
C	ARG915
C	ARG916

site_id	AC2
Number of Residues	6
Details	binding site for residue SO4 C 1202

Chain	Residue
C	LYS1117
C	GLN1120
C	GLU1137
C	MET1138
C	ARG1139
C	HOH1312

site_id	AC3
Number of Residues	2
Details	binding site for residue SO4 C 1203

Chain	Residue
C	LYS1031
D	GLN540

site_id	AC4
Number of Residues	5
Details	binding site for residue EDO C 1204

Chain	Residue
C	ARG1058
C	GLY1060
C	GLU1061
C	MET1062
C	GLU1063

site_id	AC5
Number of Residues	5
Details	binding site for residue EDO C 1205

Chain	Residue
C	HIS832
C	HIS1033
C	LYS1051
C	PHE1054
C	GLY1055

site_id	AC6
Number of Residues	5
Details	binding site for residue ZN D 2001

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

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN D 2002

Chain	Residue
D	CYS60
D	CYS62
D	CYS75
D	CYS78

site_id	AC8
Number of Residues	3
Details	binding site for residue MG D 2003

Chain	Residue
D	ASP535
D	ASP537
D	ASP539

site_id	AC9
Number of Residues	4
Details	binding site for residue SO4 D 2004

Chain	Residue
D	GLU887
D	HIS888
D	ILE990
D	ARG1267

site_id	AD1
Number of Residues	4
Details	binding site for residue SO4 D 2005

Chain	Residue
D	THR971
D	GLY972
D	ARG1160
D	ARG1164

site_id	AD2
Number of Residues	3
Details	binding site for residue SO4 D 2006

Chain	Residue
C	GLY1050
D	ARG421
D	ARG427

site_id	AD3
Number of Residues	4
Details	binding site for residue SO4 D 2007

Chain	Residue
D	ARG894
D	GLY895
D	LYS960
D	ARG1129

site_id	AD4
Number of Residues	4
Details	binding site for residue EDO D 2008

Chain	Residue
D	ARG578
D	LEU579
D	LYS689
D	ALA806

site_id	AD5
Number of Residues	2
Details	binding site for residue EDO D 2009

Chain	Residue
D	GLU1229
D	THR1230

site_id	AD6
Number of Residues	2
Details	binding site for residue EDO D 2010

Chain	Residue
D	GLY940
D	ASP942

site_id	AD7
Number of Residues	3
Details	binding site for residue SO4 F 501

Chain	Residue
F	TRP221
F	ARG224
F	ARG228

site_id	AD8
Number of Residues	4
Details	binding site for residue SO4 F 502

Chain	Residue
D	ARG389
F	MET253
F	ALA254
F	PHE255

site_id	AD9
Number of Residues	2
Details	binding site for residue SO4 F 503

Chain	Residue
F	ARG190
F	HIS232

site_id	AE1
Number of Residues	2
Details	binding site for residue SO4 F 504

Chain	Residue
F	LYS451
F	ARG457

site_id	AE2
Number of Residues	5
Details	binding site for residue SO4 F 505

Chain	Residue
D	ARG356
F	ARG268
F	GLN291
F	ALA292
O	HOH103

site_id	AE3
Number of Residues	3
Details	binding site for residue EDO F 506

Chain	Residue
F	SER406
F	ARG408
F	GLU409

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: BINDING => ECO:0000255\|HAMAP-Rule:MF_01322

Chain	Residue	Details
D	CYS60
D	CYS974
D	CYS977
D	CYS62
D	CYS75
D	CYS78
D	ASP535
D	ASP537
D	ASP539
D	CYS890
D	CYS967

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