Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4Q2U

Crystal structure of the E. coli DinJ-YafQ toxin-antitoxin complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0006351	biological_process	DNA-templated transcription
A	0006355	biological_process	regulation of DNA-templated transcription
A	0015643	molecular_function	toxic substance binding
A	0040008	biological_process	regulation of growth
A	0042803	molecular_function	protein homodimerization activity
A	0043565	molecular_function	sequence-specific DNA binding
A	0044010	biological_process	single-species biofilm formation
A	0045892	biological_process	negative regulation of DNA-templated transcription
A	0110001	cellular_component	toxin-antitoxin complex
A	2000143	biological_process	negative regulation of DNA-templated transcription initiation
B	0003677	molecular_function	DNA binding
B	0003723	molecular_function	RNA binding
B	0004519	molecular_function	endonuclease activity
B	0004521	molecular_function	RNA endonuclease activity
B	0005515	molecular_function	protein binding
B	0006402	biological_process	mRNA catabolic process
B	0006415	biological_process	translational termination
B	0016892	molecular_function	RNA endonuclease activity, producing 3'-phosphomonoesters
B	0040008	biological_process	regulation of growth
B	0043022	molecular_function	ribosome binding
B	0044010	biological_process	single-species biofilm formation
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	0046677	biological_process	response to antibiotic
B	0110001	cellular_component	toxin-antitoxin complex
C	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
C	0003677	molecular_function	DNA binding
C	0005515	molecular_function	protein binding
C	0006351	biological_process	DNA-templated transcription
C	0006355	biological_process	regulation of DNA-templated transcription
C	0015643	molecular_function	toxic substance binding
C	0040008	biological_process	regulation of growth
C	0042803	molecular_function	protein homodimerization activity
C	0043565	molecular_function	sequence-specific DNA binding
C	0044010	biological_process	single-species biofilm formation
C	0045892	biological_process	negative regulation of DNA-templated transcription
C	0110001	cellular_component	toxin-antitoxin complex
C	2000143	biological_process	negative regulation of DNA-templated transcription initiation
D	0003677	molecular_function	DNA binding
D	0003723	molecular_function	RNA binding
D	0004519	molecular_function	endonuclease activity
D	0004521	molecular_function	RNA endonuclease activity
D	0005515	molecular_function	protein binding
D	0006402	biological_process	mRNA catabolic process
D	0006415	biological_process	translational termination
D	0016892	molecular_function	RNA endonuclease activity, producing 3'-phosphomonoesters
D	0040008	biological_process	regulation of growth
D	0043022	molecular_function	ribosome binding
D	0044010	biological_process	single-species biofilm formation
D	0045892	biological_process	negative regulation of DNA-templated transcription
D	0046677	biological_process	response to antibiotic
D	0110001	cellular_component	toxin-antitoxin complex
E	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
E	0003677	molecular_function	DNA binding
E	0005515	molecular_function	protein binding
E	0006351	biological_process	DNA-templated transcription
E	0006355	biological_process	regulation of DNA-templated transcription
E	0015643	molecular_function	toxic substance binding
E	0040008	biological_process	regulation of growth
E	0042803	molecular_function	protein homodimerization activity
E	0043565	molecular_function	sequence-specific DNA binding
E	0044010	biological_process	single-species biofilm formation
E	0045892	biological_process	negative regulation of DNA-templated transcription
E	0110001	cellular_component	toxin-antitoxin complex
E	2000143	biological_process	negative regulation of DNA-templated transcription initiation
F	0003677	molecular_function	DNA binding
F	0003723	molecular_function	RNA binding
F	0004519	molecular_function	endonuclease activity
F	0004521	molecular_function	RNA endonuclease activity
F	0005515	molecular_function	protein binding
F	0006402	biological_process	mRNA catabolic process
F	0006415	biological_process	translational termination
F	0016892	molecular_function	RNA endonuclease activity, producing 3'-phosphomonoesters
F	0040008	biological_process	regulation of growth
F	0043022	molecular_function	ribosome binding
F	0044010	biological_process	single-species biofilm formation
F	0045892	biological_process	negative regulation of DNA-templated transcription
F	0046677	biological_process	response to antibiotic
F	0110001	cellular_component	toxin-antitoxin complex
G	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0006351	biological_process	DNA-templated transcription
G	0006355	biological_process	regulation of DNA-templated transcription
G	0015643	molecular_function	toxic substance binding
G	0040008	biological_process	regulation of growth
G	0042803	molecular_function	protein homodimerization activity
G	0043565	molecular_function	sequence-specific DNA binding
G	0044010	biological_process	single-species biofilm formation
G	0045892	biological_process	negative regulation of DNA-templated transcription
G	0110001	cellular_component	toxin-antitoxin complex
G	2000143	biological_process	negative regulation of DNA-templated transcription initiation
H	0003677	molecular_function	DNA binding
H	0003723	molecular_function	RNA binding
H	0004519	molecular_function	endonuclease activity
H	0004521	molecular_function	RNA endonuclease activity
H	0005515	molecular_function	protein binding
H	0006402	biological_process	mRNA catabolic process
H	0006415	biological_process	translational termination
H	0016892	molecular_function	RNA endonuclease activity, producing 3'-phosphomonoesters
H	0040008	biological_process	regulation of growth
H	0043022	molecular_function	ribosome binding
H	0044010	biological_process	single-species biofilm formation
H	0045892	biological_process	negative regulation of DNA-templated transcription
H	0046677	biological_process	response to antibiotic
H	0110001	cellular_component	toxin-antitoxin complex
I	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
I	0003677	molecular_function	DNA binding
I	0005515	molecular_function	protein binding
I	0006351	biological_process	DNA-templated transcription
I	0006355	biological_process	regulation of DNA-templated transcription
I	0015643	molecular_function	toxic substance binding
I	0040008	biological_process	regulation of growth
I	0042803	molecular_function	protein homodimerization activity
I	0043565	molecular_function	sequence-specific DNA binding
I	0044010	biological_process	single-species biofilm formation
I	0045892	biological_process	negative regulation of DNA-templated transcription
I	0110001	cellular_component	toxin-antitoxin complex
I	2000143	biological_process	negative regulation of DNA-templated transcription initiation
J	0003677	molecular_function	DNA binding
J	0003723	molecular_function	RNA binding
J	0004519	molecular_function	endonuclease activity
J	0004521	molecular_function	RNA endonuclease activity
J	0005515	molecular_function	protein binding
J	0006402	biological_process	mRNA catabolic process
J	0006415	biological_process	translational termination
J	0016892	molecular_function	RNA endonuclease activity, producing 3'-phosphomonoesters
J	0040008	biological_process	regulation of growth
J	0043022	molecular_function	ribosome binding
J	0044010	biological_process	single-species biofilm formation
J	0045892	biological_process	negative regulation of DNA-templated transcription
J	0046677	biological_process	response to antibiotic
J	0110001	cellular_component	toxin-antitoxin complex
K	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
K	0003677	molecular_function	DNA binding
K	0005515	molecular_function	protein binding
K	0006351	biological_process	DNA-templated transcription
K	0006355	biological_process	regulation of DNA-templated transcription
K	0015643	molecular_function	toxic substance binding
K	0040008	biological_process	regulation of growth
K	0042803	molecular_function	protein homodimerization activity
K	0043565	molecular_function	sequence-specific DNA binding
K	0044010	biological_process	single-species biofilm formation
K	0045892	biological_process	negative regulation of DNA-templated transcription
K	0110001	cellular_component	toxin-antitoxin complex
K	2000143	biological_process	negative regulation of DNA-templated transcription initiation
L	0003677	molecular_function	DNA binding
L	0003723	molecular_function	RNA binding
L	0004519	molecular_function	endonuclease activity
L	0004521	molecular_function	RNA endonuclease activity
L	0005515	molecular_function	protein binding
L	0006402	biological_process	mRNA catabolic process
L	0006415	biological_process	translational termination
L	0016892	molecular_function	RNA endonuclease activity, producing 3'-phosphomonoesters
L	0040008	biological_process	regulation of growth
L	0043022	molecular_function	ribosome binding
L	0044010	biological_process	single-species biofilm formation
L	0045892	biological_process	negative regulation of DNA-templated transcription
L	0046677	biological_process	response to antibiotic
L	0110001	cellular_component	toxin-antitoxin complex
M	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
M	0003677	molecular_function	DNA binding
M	0005515	molecular_function	protein binding
M	0006351	biological_process	DNA-templated transcription
M	0006355	biological_process	regulation of DNA-templated transcription
M	0015643	molecular_function	toxic substance binding
M	0040008	biological_process	regulation of growth
M	0042803	molecular_function	protein homodimerization activity
M	0043565	molecular_function	sequence-specific DNA binding
M	0044010	biological_process	single-species biofilm formation
M	0045892	biological_process	negative regulation of DNA-templated transcription
M	0110001	cellular_component	toxin-antitoxin complex
M	2000143	biological_process	negative regulation of DNA-templated transcription initiation
N	0003677	molecular_function	DNA binding
N	0003723	molecular_function	RNA binding
N	0004519	molecular_function	endonuclease activity
N	0004521	molecular_function	RNA endonuclease activity
N	0005515	molecular_function	protein binding
N	0006402	biological_process	mRNA catabolic process
N	0006415	biological_process	translational termination
N	0016892	molecular_function	RNA endonuclease activity, producing 3'-phosphomonoesters
N	0040008	biological_process	regulation of growth
N	0043022	molecular_function	ribosome binding
N	0044010	biological_process	single-species biofilm formation
N	0045892	biological_process	negative regulation of DNA-templated transcription
N	0046677	biological_process	response to antibiotic
N	0110001	cellular_component	toxin-antitoxin complex
O	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
O	0003677	molecular_function	DNA binding
O	0005515	molecular_function	protein binding
O	0006351	biological_process	DNA-templated transcription
O	0006355	biological_process	regulation of DNA-templated transcription
O	0015643	molecular_function	toxic substance binding
O	0040008	biological_process	regulation of growth
O	0042803	molecular_function	protein homodimerization activity
O	0043565	molecular_function	sequence-specific DNA binding
O	0044010	biological_process	single-species biofilm formation
O	0045892	biological_process	negative regulation of DNA-templated transcription
O	0110001	cellular_component	toxin-antitoxin complex
O	2000143	biological_process	negative regulation of DNA-templated transcription initiation
P	0003677	molecular_function	DNA binding
P	0003723	molecular_function	RNA binding
P	0004519	molecular_function	endonuclease activity
P	0004521	molecular_function	RNA endonuclease activity
P	0005515	molecular_function	protein binding
P	0006402	biological_process	mRNA catabolic process
P	0006415	biological_process	translational termination
P	0016892	molecular_function	RNA endonuclease activity, producing 3'-phosphomonoesters
P	0040008	biological_process	regulation of growth
P	0043022	molecular_function	ribosome binding
P	0044010	biological_process	single-species biofilm formation
P	0045892	biological_process	negative regulation of DNA-templated transcription
P	0046677	biological_process	response to antibiotic
P	0110001	cellular_component	toxin-antitoxin complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 101

Chain	Residue
A	ALA5
A	PHE6
A	ARG8
A	HOH219
A	HOH244
O	LYS16

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 102

Chain	Residue
A	HOH286
A	HOH289
G	LYS63
O	ARG43
A	ARG52
A	GLU53
A	HOH205

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 103

Chain	Residue
A	ASN55
A	GLN56
A	HOH205
A	HOH228
B	HOH269
G	GLN56

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 104

Chain	Residue
A	SER31
A	ARG35
M	ARG10
O	ARG10

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 101

Chain	Residue
B	PRO51
B	ARG60
B	HOH212
B	HOH214
B	HOH223
B	HOH240
P	PRO51
P	ARG60

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 B 102

Chain	Residue
A	PHE49
A	ASP50
A	HOH201
B	HIS50
B	ASP61
B	HIS63
B	HIS87
B	HOH204
B	HOH210

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 103

Chain	Residue
A	GLU66
B	LYS73
B	LEU78
B	ARG80
B	HOH215
M	LYS45

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 104

Chain	Residue
B	PRO44
B	ALA45
B	HOH217

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 105

Chain	Residue
B	ARG22
B	LYS24
B	HOH213
B	HOH220
B	HOH249

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 106

Chain	Residue
B	THR86
B	ALA88
B	HOH236
J	LYS14

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 101

Chain	Residue
C	ASN55
C	GLN56
C	HOH208
C	HOH229
C	HOH239
C	HOH261
D	HOH257
E	GLN56

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 102

Chain	Residue
C	HOH250
C	HOH253
C	HOH258
E	PHE6
E	ARG8
I	LYS16

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 103

Chain	Residue
C	PHE6
C	ARG8
C	HOH244
C	HOH272
G	HOH228
K	LYS16

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 104

Chain	Residue
C	SER31
C	ARG35
I	ARG10
K	ARG10

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 D 101

Chain	Residue
D	PRO51
D	ARG60
D	HOH206
D	HOH223
D	HOH229
D	HOH231
L	PRO51
L	ARG60

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 D 102

Chain	Residue
C	GLU66
C	HOH207
D	LYS73
D	LEU78
D	ARG80
D	HOH286
I	LYS45

site_id	BC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 D 103

Chain	Residue
C	HOH201
D	HIS50
D	ASP61
D	HIS63
D	HIS87
D	HOH207
D	HOH213
C	PHE49
C	ASP50

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 104

Chain	Residue
D	PRO44
D	ALA45
D	HOH209

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 D 105

Chain	Residue
D	ARG22
D	THR86
D	HOH205
D	HOH265
D	HOH288

site_id	CC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 E 101

Chain	Residue
C	LYS63
E	ARG52
E	GLU53
E	HOH204
E	HOH207
E	HOH257
E	HOH261
I	ARG43

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 102

Chain	Residue
C	GLN56
C	HOH234
E	ASN55
E	GLN56
E	HOH204
E	HOH231
F	HOH261

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 103

Chain	Residue
E	SER31
E	ARG35
I	ARG10

site_id	CC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 F 101

Chain	Residue
E	PHE49
E	ASP50
E	HOH201
F	HIS50
F	ASP61
F	HIS63
F	HIS87
F	HOH202
F	HOH203

site_id	CC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 F 102

Chain	Residue
F	PRO51
F	ARG60
F	HOH211
F	HOH212
F	HOH232
F	HOH237
F	HOH265
J	PRO51
J	ARG60

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 F 103

Chain	Residue
C	HOH213
E	GLU66
F	LYS73
F	LEU78
F	ARG80
F	HOH283
K	LYS45

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 F 104

Chain	Residue
B	HOH218
F	PRO44
F	ALA45
F	HOH208

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 F 105

Chain	Residue
F	ARG22
F	LYS24
F	HOH214
F	HOH245
F	HOH285

site_id	DC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 G 101

Chain	Residue
A	LYS63
G	ARG52
G	GLU53
G	HOH210
G	HOH211
G	HOH269
G	HOH284
M	ARG43
M	HOH202

site_id	DC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 G 102

Chain	Residue
A	GLN56
A	HOH249
G	ASN55
G	GLN56
G	HOH210
G	HOH226
G	HOH232

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 G 103

Chain	Residue
G	ALA5
G	PHE6
G	ARG8
G	HOH227
G	HOH256
M	LYS16

site_id	DC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 G 104

Chain	Residue
G	SER31
G	ARG35
K	ARG10
M	ARG10

site_id	DC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 H 101

Chain	Residue
G	PHE49
G	ASP50
G	HOH286
H	HIS50
H	ASP61
H	HIS63
H	HIS87
H	HOH204
H	HOH217

site_id	DC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 H 102

Chain	Residue
H	PRO51
H	ARG60
H	HOH211
H	HOH216
H	HOH223
H	HOH241
N	PRO51
N	ARG60

site_id	DC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 H 103

Chain	Residue
G	GLU66
G	HOH205
H	LYS73
H	LEU78
H	ARG80
H	HOH279
O	LYS45

site_id	DC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 H 104

Chain	Residue
H	PRO44
H	ALA45
H	HOH210

site_id	DC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 H 105

Chain	Residue
H	ARG22
H	THR86
H	ALA89
H	HOH206
H	HOH252

site_id	EC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 H 106

Chain	Residue
H	LYS24
H	HOH227
H	HOH234
H	HOH275
H	HOH278

site_id	EC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 I 101

Chain	Residue
E	ALA9
E	ARG10
I	SER31
I	ARG35
I	HOH228
L	THR86
L	ALA88
L	ALA89
L	HOH231

site_id	EC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 J 101

Chain	Residue
I	PHE49
I	ASP50
I	HOH204
I	HOH256
J	HIS50
J	ASP61
J	HIS63
J	HIS87
J	HOH204
J	HOH215

site_id	EC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 J 102

Chain	Residue
J	PRO44
J	ALA45
J	HOH236
L	PRO44
L	ALA45
L	HOH253

site_id	EC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 K 101

Chain	Residue
C	ARG52
C	GLU53
C	HOH208
E	LYS63
K	ARG43
K	HOH208
K	HOH220
K	HOH260

site_id	EC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 L 101

Chain	Residue
K	PHE49
K	ASP50
K	HOH204
L	HIS50
L	ASP61
L	HIS63
L	HIS87
L	HOH202
L	HOH214

site_id	EC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 L 102

Chain	Residue
E	ARG10
L	ARG22
L	LYS24
L	HOH224

site_id	EC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SO4 M 101

Chain	Residue
G	ARG8
G	ALA9
G	ARG10
M	SER31
M	ARG35
M	HOH221
M	HOH227
P	ARG22
P	THR86
P	ALA88
P	ALA89

site_id	EC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 N 101

Chain	Residue
M	ASP50
N	HIS50
N	ASP61
N	HIS63
N	HIS87
N	HOH205
N	HOH209
N	HOH223

site_id	FC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 N 102

Chain	Residue
C	ALA9
C	ARG10
C	HOH221
K	SER31
K	ARG35
N	THR86
N	ALA88
N	ALA89
N	HOH211
N	HOH220

site_id	FC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 O 101

Chain	Residue
A	ALA9
A	ARG10
A	HOH290
J	THR86
J	ALA88
J	ALA89
O	SER31
O	ARG35
O	HOH208
O	HOH210

site_id	FC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 P 101

Chain	Residue
O	PHE49
O	ASP50
O	HOH217
O	HOH223
O	HOH253
P	HIS50
P	ASP61
P	HIS63
P	HIS87
P	HOH205

site_id	FC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 P 102

Chain	Residue
N	PRO44
N	ALA45
P	PRO44
P	ALA45
P	HOH229

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Proton donor => ECO:0000305

Chain	Residue	Details
B	HIS87
D	HIS87
F	HIS87
H	HIS87
J	HIS87
L	HIS87
N	HIS87
P	HIS87

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