Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3MLE

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion binding
A	0004141	molecular_function	dethiobiotin synthase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0009102	biological_process	biotin biosynthetic process
A	0016874	molecular_function	ligase activity
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide binding
B	0000287	molecular_function	magnesium ion binding
B	0004141	molecular_function	dethiobiotin synthase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0009102	biological_process	biotin biosynthetic process
B	0016874	molecular_function	ligase activity
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0000287	molecular_function	magnesium ion binding
C	0004141	molecular_function	dethiobiotin synthase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0009102	biological_process	biotin biosynthetic process
C	0016874	molecular_function	ligase activity
C	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide binding
D	0000287	molecular_function	magnesium ion binding
D	0004141	molecular_function	dethiobiotin synthase activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0009102	biological_process	biotin biosynthetic process
D	0016874	molecular_function	ligase activity
D	0046872	molecular_function	metal ion binding
E	0000166	molecular_function	nucleotide binding
E	0000287	molecular_function	magnesium ion binding
E	0004141	molecular_function	dethiobiotin synthase activity
E	0005524	molecular_function	ATP binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0009102	biological_process	biotin biosynthetic process
E	0016874	molecular_function	ligase activity
E	0046872	molecular_function	metal ion binding
F	0000166	molecular_function	nucleotide binding
F	0000287	molecular_function	magnesium ion binding
F	0004141	molecular_function	dethiobiotin synthase activity
F	0005524	molecular_function	ATP binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0009102	biological_process	biotin biosynthetic process
F	0016874	molecular_function	ligase activity
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 A 221

Chain	Residue
A	THR9
C	8AC224
A	LYS13
A	LYS35
A	ASP50
A	GLU116
A	ALA118
A	GLY119
A	MG222
A	ADP226

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 222

Chain	Residue
A	THR14
A	ASP50
A	GLU116
A	PO4221
A	ADP226

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NO3 A 223

Chain	Residue
A	VAL41
A	ASN42
A	ASP43
A	ARG74
A	TYR75
A	HIS76

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL A 224

Chain	Residue
A	GLN22
B	GLN22

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 8AC A 225

Chain	Residue
A	LEU150
A	GLY151
A	LEU152
A	ILE153
A	ASN154
C	THR9
C	THR39
C	SER79
C	PO4221

site_id	AC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ADP A 226

Chain	Residue
A	ASN10
A	ALA11
A	GLY12
A	LYS13
A	THR14
A	THR15
A	GLU116
A	ASN175
A	GLN206
A	PO4221
A	MG222
A	HOH230
B	ARG63

site_id	AC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 B 221

Chain	Residue
B	THR9
B	LYS13
B	LYS35
B	ASP50
B	GLU116
B	ALA118
B	GLY119
B	MG222
B	PO4224
B	ADP226
D	8AC224

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG B 222

Chain	Residue
B	THR14
B	LYS35
B	ASP50
B	GLU116
B	PO4221
B	PO4224
B	ADP226

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NO3 B 223

Chain	Residue
B	VAL41
B	ASN42
B	ASP43
B	ARG74
B	HIS76

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 B 224

Chain	Residue
B	ASN10
B	ALA11
B	GLY12
B	LYS13
B	THR14
B	GLU116
B	PO4221
B	MG222

site_id	BC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 8AC B 225

Chain	Residue
B	GLY151
B	LEU152
B	ILE153
B	ASN154
D	THR9
D	THR39
D	SER79
D	ALA80
D	PO4221

site_id	BC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ADP B 226

Chain	Residue
A	ARG63
B	ASN10
B	ALA11
B	GLY12
B	LYS13
B	THR14
B	THR15
B	GLU116
B	ASN175
B	GLN206
B	PO4221
B	MG222

site_id	BC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 C 221

Chain	Residue
C	LYS13
C	LYS35
C	ASP50
C	GLU116
C	ALA118
C	GLY119
C	MG222
C	ADP225
A	8AC225
C	THR9

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 222

Chain	Residue
C	THR14
C	ASP50
C	GLU116
C	PO4221
C	ADP225

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL C 223

Chain	Residue
C	GLN22
E	GLN22
E	ASP57

site_id	BC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE 8AC C 224

Chain	Residue
A	THR9
A	THR39
A	SER79
A	VAL123
A	PO4221
C	LEU150
C	GLY151
C	LEU152
C	ILE153
C	ASN154

site_id	BC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ADP C 225

Chain	Residue
C	ASN10
C	ALA11
C	GLY12
C	LYS13
C	THR14
C	THR15
C	GLU116
C	ASN175
C	LYS177
C	PO4221
C	MG222
C	HOH232
E	ARG63

site_id	BC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 D 221

Chain	Residue
B	8AC225
D	THR9
D	LYS13
D	LYS35
D	ASP50
D	GLU116
D	ALA118
D	GLY119
D	MG222
D	PO4223
D	ADP225

site_id	CC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG D 222

Chain	Residue
D	THR14
D	LYS35
D	ASP50
D	GLU116
D	PO4221
D	PO4223
D	ADP225

site_id	CC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 D 223

Chain	Residue
D	ASN10
D	ALA11
D	GLY12
D	LYS13
D	THR14
D	GLU116
D	PO4221
D	MG222

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 8AC D 224

Chain	Residue
B	THR9
B	THR39
B	VAL123
B	PO4221
D	GLY151
D	LEU152
D	ILE153
D	ASN154

site_id	CC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ADP D 225

Chain	Residue
D	ASN10
D	ALA11
D	GLY12
D	LYS13
D	THR14
D	THR15
D	GLU116
D	ASN175
D	LYS177
D	PO4221
D	MG222
F	ARG63

site_id	CC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 E 221

Chain	Residue
E	THR9
E	LYS13
E	LYS35
E	ASP50
E	GLU116
E	GLY119
E	MG222
E	ADP223
E	HOH236
F	8AC225

site_id	CC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG E 222

Chain	Residue
E	THR14
E	LYS35
E	ASP50
E	GLU116
E	PO4221
E	ADP223
E	HOH236

site_id	CC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ADP E 223

Chain	Residue
C	ARG63
E	ASN10
E	ALA11
E	GLY12
E	LYS13
E	THR14
E	THR15
E	GLU116
E	ASN175
E	LYS177
E	GLN206
E	PO4221
E	MG222
E	HOH228
E	HOH229
E	HOH236

site_id	CC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 8AC E 224

Chain	Residue
E	LEU150
E	GLY151
E	LEU152
E	ILE153
E	ASN154
F	THR9
F	THR39
F	SER79
F	GLY119
F	VAL123
F	PO4221

site_id	CC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 F 221

Chain	Residue
E	8AC224
F	THR9
F	LYS13
F	LYS35
F	ASP50
F	GLU116
F	ALA118
F	GLY119
F	MG222
F	ADP226

site_id	DC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG F 222

Chain	Residue
F	THR14
F	ASP50
F	GLU116
F	PO4221
F	ADP226

site_id	DC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NO3 F 223

Chain	Residue
F	ASN42
F	ASP43
F	ARG74
F	HIS76

site_id	DC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL F 224

Chain	Residue
D	GLN22
F	GLN22

site_id	DC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE 8AC F 225

Chain	Residue
E	THR9
E	THR39
E	PO4221
F	LEU150
F	GLY151
F	ILE153
F	ASN154

site_id	DC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ADP F 226

Chain	Residue
D	ARG63
F	ASN10
F	ALA11
F	GLY12
F	LYS13
F	THR14
F	THR15
F	GLU116
F	ASN175
F	LYS177
F	PO4221
F	MG222

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXS","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QY0","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QY0","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QY0","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QY0","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3QXC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXS","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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