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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3QY0

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

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
A	0016874	molecular_function	ligase activity
A	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE GDP A 221

Chain	Residue
A	ASN10
A	MG223
A	MG224
A	HOH270
A	HOH326
A	HOH338
A	HOH420
A	ALA11
A	GLY12
A	LYS13
A	THR14
A	THR15
A	GLU116
A	GLN167
A	PO4222

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PO4 A 222

Chain	Residue
A	THR9
A	LYS13
A	LYS35
A	ASP50
A	GLU116
A	GLY119
A	GDP221
A	MG223
A	MG224
A	HOH270
A	HOH413
A	HOH429
A	HOH430

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MG A 223

Chain	Residue
A	THR9
A	GDP221
A	PO4222
A	MG224
A	HOH270
A	HOH420
A	HOH429
A	HOH430

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG A 224

Chain	Residue
A	THR14
A	ASP50
A	GLU116
A	GDP221
A	PO4222
A	MG223
A	HOH270

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 225

Chain	Residue
A	ASN130
A	LEU132
A	ASP133
A	EDO239
A	HOH315

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

Chain	Residue
A	PHE72
A	TYR73
A	ARG74
A	TYR75
A	ASP89
A	HOH436

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 227

Chain	Residue
A	LYS171
A	HIS184
A	ASN200
A	PRO201
A	HOH262
A	HOH383

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 228

Chain	Residue
A	THR39
A	SER79
A	PRO81
A	GLY119
A	VAL123

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 229

Chain	Residue
A	LYS139
A	ALA140
A	LYS141
A	LEU168
A	ASP169
A	HOH390

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 230

Chain	Residue
A	GLY178
A	THR181
A	ASN195
A	ASN199
A	GLN207
A	HOH244

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 231

Chain	Residue
A	ASN42
A	ASP43
A	ARG74
A	HIS76

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 232

Chain	Residue
A	THR7
A	ASN8
A	THR9
A	GLY119
A	GLY151
A	ASN154
A	ASP155
A	HOH290

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 233

Chain	Residue
A	ASN25
A	GLY28
A	LEU61
A	HOH428

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 234

Chain	Residue
A	GLN22
A	ASP57

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 235

Chain	Residue
A	TYR73
A	ALA92
A	PRO93
A	HOH398

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 236

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

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

Chain	Residue
A	CYS122
A	ASN130
A	LEU157
A	TYR190
A	HOH315
A	HOH356

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 238

Chain	Residue
A	PHE-3
A	HIS0
A	GLU87
A	GLU88
A	LEU217
A	GLY219

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 239

Chain	Residue
A	LEU157
A	ASP160
A	PHE161
A	LYS164
A	EDO225

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 240

Chain	Residue
A	SER64
A	ASP89
A	PRO90
A	ASN91
A	HOH340

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	ACT_SITE: ACT_SITE => ECO:0000255\|HAMAP-Rule:MF_00336, ECO:0000305\|PubMed:22284390

Chain	Residue	Details
A	LYS35

site_id	SWS_FT_FI2
Number of Residues	1
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00336, ECO:0000269\|PubMed:22284390, ECO:0007744\|PDB:3MLE, ECO:0007744\|PDB:3QXC, ECO:0007744\|PDB:3QXH, ECO:0007744\|PDB:3QXJ, ECO:0007744\|PDB:3QXS

Chain	Residue	Details
A	THR9

site_id	SWS_FT_FI3
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00336, ECO:0000269\|PubMed:22284390, ECO:0007744\|PDB:3MLE, ECO:0007744\|PDB:3QXC, ECO:0007744\|PDB:3QXH, ECO:0007744\|PDB:3QXJ, ECO:0007744\|PDB:3QXS, ECO:0007744\|PDB:3QXX, ECO:0007744\|PDB:3QY0

Chain	Residue	Details
A	THR14
A	GLU116

site_id	SWS_FT_FI4
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:22284390, ECO:0007744\|PDB:3MLE, ECO:0007744\|PDB:3QXH, ECO:0007744\|PDB:3QXX, ECO:0007744\|PDB:3QY0

Chain	Residue	Details
A	LYS35

site_id	SWS_FT_FI5
Number of Residues	1
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00336, ECO:0000269\|PubMed:22284390

Chain	Residue	Details
A	THR39

site_id	SWS_FT_FI6
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:22284390, ECO:0007744\|PDB:3MLE, ECO:0007744\|PDB:3QXC, ECO:0007744\|PDB:3QXH, ECO:0007744\|PDB:3QXJ, ECO:0007744\|PDB:3QXS, ECO:0007744\|PDB:3QXX, ECO:0007744\|PDB:3QY0

Chain	Residue	Details
A	ASP50

site_id	SWS_FT_FI7
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:22284390, ECO:0007744\|PDB:3MLE

Chain	Residue	Details
A	GLY151

site_id	SWS_FT_FI8
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:22284390, ECO:0007744\|PDB:3QXC, ECO:0007744\|PDB:3QXS

Chain	Residue	Details
A	ASN175

226707

PDB entries from 2024-10-30

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