Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5DED

Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005524	molecular_function	ATP binding
A	0005525	molecular_function	GTP binding
A	0008728	molecular_function	GTP diphosphokinase activity
A	0015969	biological_process	guanosine tetraphosphate metabolic process
A	0015970	biological_process	guanosine tetraphosphate biosynthetic process
A	0016301	molecular_function	kinase activity
A	0016310	biological_process	phosphorylation
A	0046872	molecular_function	metal ion binding
B	0005524	molecular_function	ATP binding
B	0005525	molecular_function	GTP binding
B	0008728	molecular_function	GTP diphosphokinase activity
B	0015969	biological_process	guanosine tetraphosphate metabolic process
B	0015970	biological_process	guanosine tetraphosphate biosynthetic process
B	0016301	molecular_function	kinase activity
B	0016310	biological_process	phosphorylation
B	0046872	molecular_function	metal ion binding
C	0005524	molecular_function	ATP binding
C	0005525	molecular_function	GTP binding
C	0008728	molecular_function	GTP diphosphokinase activity
C	0015969	biological_process	guanosine tetraphosphate metabolic process
C	0015970	biological_process	guanosine tetraphosphate biosynthetic process
C	0016301	molecular_function	kinase activity
C	0016310	biological_process	phosphorylation
C	0046872	molecular_function	metal ion binding
D	0005524	molecular_function	ATP binding
D	0005525	molecular_function	GTP binding
D	0008728	molecular_function	GTP diphosphokinase activity
D	0015969	biological_process	guanosine tetraphosphate metabolic process
D	0015970	biological_process	guanosine tetraphosphate biosynthetic process
D	0016301	molecular_function	kinase activity
D	0016310	biological_process	phosphorylation
D	0046872	molecular_function	metal ion binding
E	0005524	molecular_function	ATP binding
E	0005525	molecular_function	GTP binding
E	0008728	molecular_function	GTP diphosphokinase activity
E	0015969	biological_process	guanosine tetraphosphate metabolic process
E	0015970	biological_process	guanosine tetraphosphate biosynthetic process
E	0016301	molecular_function	kinase activity
E	0016310	biological_process	phosphorylation
E	0046872	molecular_function	metal ion binding
F	0005524	molecular_function	ATP binding
F	0005525	molecular_function	GTP binding
F	0008728	molecular_function	GTP diphosphokinase activity
F	0015969	biological_process	guanosine tetraphosphate metabolic process
F	0015970	biological_process	guanosine tetraphosphate biosynthetic process
F	0016301	molecular_function	kinase activity
F	0016310	biological_process	phosphorylation
F	0046872	molecular_function	metal ion binding
G	0005524	molecular_function	ATP binding
G	0005525	molecular_function	GTP binding
G	0008728	molecular_function	GTP diphosphokinase activity
G	0015969	biological_process	guanosine tetraphosphate metabolic process
G	0015970	biological_process	guanosine tetraphosphate biosynthetic process
G	0016301	molecular_function	kinase activity
G	0016310	biological_process	phosphorylation
G	0046872	molecular_function	metal ion binding
H	0005524	molecular_function	ATP binding
H	0005525	molecular_function	GTP binding
H	0008728	molecular_function	GTP diphosphokinase activity
H	0015969	biological_process	guanosine tetraphosphate metabolic process
H	0015970	biological_process	guanosine tetraphosphate biosynthetic process
H	0016301	molecular_function	kinase activity
H	0016310	biological_process	phosphorylation
H	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	16
Details	binding site for residue 0O2 D 301

Chain	Residue
D	ARG46
D	TYR116
D	HIS120
D	GLU139
D	GLN141
D	ALA151
D	GLU154
D	HIS155
D	LYS48
D	LYS56
D	ARG59
D	ASP72
D	ARG105
D	TYR107
D	LYS112
D	SER114

site_id	AC2
Number of Residues	12
Details	binding site for residue 0O2 D 302

Chain	Residue
B	LYS21
B	LYS25
B	ARG28
B	PHE42
B	THR44
B	ASN148
B	MG302
D	LYS21
D	LYS25
D	GLU41
D	PHE42
D	THR44

site_id	AC3
Number of Residues	17
Details	binding site for residue 0O2 A 301

Chain	Residue
A	ARG46
A	LYS48
A	LYS56
A	ARG59
A	LYS60
A	ASP72
A	ARG105
A	TYR107
A	LYS112
A	SER114
A	TYR116
A	HIS120
A	GLU139
A	GLN141
A	ALA151
A	GLU154
A	HIS155

site_id	AC4
Number of Residues	12
Details	binding site for residue 0O2 A 302

Chain	Residue
A	LYS21
A	LYS25
A	GLU41
A	PHE42
A	VAL43
A	MG303
C	LYS21
C	LYS25
C	ARG28
C	PHE42
C	THR44
C	ASN148

site_id	AC5
Number of Residues	1
Details	binding site for residue MG A 303

Chain	Residue
A	0O2302

site_id	AC6
Number of Residues	17
Details	binding site for residue 0O2 B 301

Chain	Residue
B	ARG46
B	LYS48
B	LYS56
B	ARG59
B	LYS60
B	ASP72
B	ARG105
B	TYR107
B	LYS112
B	SER114
B	TYR116
B	HIS120
B	GLU139
B	GLN141
B	ALA151
B	GLU154
B	HIS155

site_id	AC7
Number of Residues	1
Details	binding site for residue MG B 302

Chain	Residue
D	0O2302

site_id	AC8
Number of Residues	17
Details	binding site for residue 0O2 C 301

Chain	Residue
C	ARG46
C	LYS48
C	LYS56
C	ARG59
C	LYS60
C	ASP72
C	ARG105
C	TYR107
C	LYS112
C	SER114
C	TYR116
C	HIS120
C	GLU139
C	GLN141
C	ALA151
C	GLU154
C	HIS155

site_id	AC9
Number of Residues	14
Details	binding site for residue 0O2 E 301

Chain	Residue
E	SER114
E	TYR116
E	HIS120
E	GLU139
E	GLN141
E	ALA151
E	GLU154
E	HIS155
E	ARG46
E	LYS48
E	LYS60
E	ARG105
E	TYR107
E	LYS112

site_id	AD1
Number of Residues	1
Details	binding site for residue MG E 302

Chain	Residue
H	0O2302

site_id	AD2
Number of Residues	16
Details	binding site for residue 0O2 F 301

Chain	Residue
F	LYS48
F	LYS56
F	ARG59
F	ASP72
F	ARG77
F	ARG105
F	TYR107
F	LYS112
F	SER114
F	TYR116
F	HIS120
F	GLU139
F	GLN141
F	ALA151
F	GLU154
F	HIS155

site_id	AD3
Number of Residues	16
Details	binding site for residue 0O2 G 301

Chain	Residue
G	ARG46
G	LYS48
G	LYS56
G	ARG59
G	ASP72
G	ARG105
G	TYR107
G	LYS112
G	SER114
G	TYR116
G	HIS120
G	GLU139
G	GLN141
G	ALA151
G	GLU154
G	HIS155

site_id	AD4
Number of Residues	11
Details	binding site for residue 0O2 G 302

Chain	Residue
F	LYS21
F	LYS25
F	ARG28
F	PHE42
F	THR44
G	LYS25
G	ARG28
G	GLU41
G	PHE42
G	THR44
G	MG303

site_id	AD5
Number of Residues	1
Details	binding site for residue MG G 303

Chain	Residue
G	0O2302

site_id	AD6
Number of Residues	17
Details	binding site for residue 0O2 H 301

Chain	Residue
H	ARG46
H	LYS48
H	LYS56
H	ARG59
H	LYS60
H	ASP72
H	ARG105
H	TYR107
H	LYS112
H	SER114
H	TYR116
H	HIS120
H	GLU139
H	GLN141
H	ALA151
H	GLU154
H	HIS155

site_id	AD7
Number of Residues	14
Details	binding site for residue 0O2 H 302

Chain	Residue
E	LYS21
E	LYS25
E	ARG28
E	PHE42
E	THR44
E	ASN148
E	MG302
H	LYS21
H	LYS25
H	ARG28
H	GLU41
H	PHE42
H	VAL43
H	THR44

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Proton acceptor => ECO:0000305\|PubMed:26460002

Chain	Residue	Details
D	GLU139
A	GLU139
B	GLU139
C	GLU139
E	GLU139
F	GLU139
G	GLU139
H	GLU139

site_id	SWS_FT_FI2
Number of Residues	72
Details	BINDING: BINDING => ECO:0000269\|PubMed:26460002, ECO:0007744\|PDB:5DED

Chain	Residue	Details
D	LYS21
A	LYS21
A	GLU41
A	ARG46
A	ARG59
A	ARG105
A	LYS112
A	HIS120
A	ASN148
A	ALA151
B	LYS21
D	GLU41
B	GLU41
B	ARG46
B	ARG59
B	ARG105
B	LYS112
B	HIS120
B	ASN148
B	ALA151
C	LYS21
C	GLU41
D	ARG46
C	ARG46
C	ARG59
C	ARG105
C	LYS112
C	HIS120
C	ASN148
C	ALA151
E	LYS21
E	GLU41
E	ARG46
D	ARG59
E	ARG59
E	ARG105
E	LYS112
E	HIS120
E	ASN148
E	ALA151
F	LYS21
F	GLU41
F	ARG46
F	ARG59
D	ARG105
F	ARG105
F	LYS112
F	HIS120
F	ASN148
F	ALA151
G	LYS21
G	GLU41
G	ARG46
G	ARG59
G	ARG105
D	LYS112
G	LYS112
G	HIS120
G	ASN148
G	ALA151
H	LYS21
H	GLU41
H	ARG46
H	ARG59
H	ARG105
H	LYS112
D	HIS120
H	HIS120
H	ASN148
H	ALA151
D	ASN148
D	ALA151

site_id	SWS_FT_FI3
Number of Residues	24
Details	BINDING: BINDING => ECO:0000305\|PubMed:26460002, ECO:0007744\|PDB:5F2V

Chain	Residue	Details
D	SER52
C	SER52
C	LYS56
C	ARG77
E	SER52
E	LYS56
E	ARG77
F	SER52
F	LYS56
F	ARG77
G	SER52
D	LYS56
G	LYS56
G	ARG77
H	SER52
H	LYS56
H	ARG77
D	ARG77
A	SER52
A	LYS56
A	ARG77
B	SER52
B	LYS56
B	ARG77

site_id	SWS_FT_FI4
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:26460002

Chain	Residue	Details
D	ASP72
A	ASP72
B	ASP72
C	ASP72
E	ASP72
F	ASP72
G	ASP72
H	ASP72

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