Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3QXC

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

Functional Information from GO Data

Chain	GOid	namespace	contents
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

Functional Information from PDB Data

site_id	AC1
Number of Residues	23
Details	BINDING SITE FOR RESIDUE ATP A 221

Chain	Residue
A	THR9
A	GLU116
A	GLN167
A	ASN175
A	LYS177
A	MG222
A	HOH278
A	HOH291
A	HOH294
A	HOH358
A	HOH362
A	ASN10
A	HOH366
A	HOH412
A	HOH486
A	HOH559
A	ALA11
A	GLY12
A	LYS13
A	THR14
A	THR15
A	LYS35
A	ASP50

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

Chain	Residue
A	THR14
A	ASP50
A	GLU116
A	ATP221
A	HOH362

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NO3 A 223

Chain	Residue
A	SER5
A	ALA6
A	LYS13
A	GLY117
A	ALA118
A	GLY119
A	GLY120
A	LEU121
A	MET131
A	HOH284

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 224

Chain	Residue
A	ASN130
A	LEU132
A	ASP133
A	LEU162
A	HIS166
A	HOH254

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 225

Chain	Residue
A	ASN42
A	ASP43
A	ARG74
A	HIS76
A	HOH288
A	HOH499

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 226

Chain	Residue
A	ASN25
A	GLY28
A	LYS30
A	LEU61
A	HOH258
A	HOH272

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 227

Chain	Residue
A	HIS0
A	MET1
A	LYS139
A	LYS141
A	SER220

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 228

Chain	Residue
A	GLN22
A	ASP57
A	HOH536

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 229

Chain	Residue
A	ASN179
A	ASN180
A	THR181
A	ALA182
A	HOH247
A	HOH328
A	HOH509
A	HOH558

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 230

Chain	Residue
A	ASN8
A	HIS147
A	ASN149
A	HOH466

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 231

Chain	Residue
A	LEU157
A	ASP160
A	PHE161
A	LYS164
A	HOH254
A	HOH271

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 232

Chain	Residue
A	LEU168
A	ASP169
A	TYR170
A	ASN200
A	HOH270
A	HOH432

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 233

Chain	Residue
A	CYS122
A	GLU129
A	ASN130
A	LEU157
A	TYR190
A	HOH254
A	HOH397
A	HOH435

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 234

Chain	Residue
A	HOH551
A	ASN199
A	ILE202
A	HOH255

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 235

Chain	Residue
A	THR9
A	THR39
A	GLY40
A	VAL78
A	SER79
A	HOH294

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PEG A 236

Chain	Residue
A	LYS171
A	HIS184
A	ASN199
A	ASN200
A	PRO201
A	VAL211
A	HOH310
A	HOH398

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 237

Chain	Residue
A	PHE72
A	TYR73
A	ARG74
A	TYR75
A	ASP89
A	HOH282

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
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	6
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	2
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	1
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	1
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	1
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	3
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	3
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	2
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	1
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)