3QY0

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

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

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	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

---