3QXJ

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

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	20
Details	BINDING SITE FOR RESIDUE GTP A 221

Chain	Residue
A	THR9
A	GLU116
A	GLN167
A	MG224
A	EDO232
A	HOH279
A	HOH283
A	HOH284
A	HOH374
A	HOH468
A	HOH492
A	ASN10
A	HOH520
A	ALA11
A	GLY12
A	LYS13
A	THR14
A	THR15
A	LYS35
A	ASP50

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 222

Chain	Residue
A	ASN42
A	ASP43
A	ARG74
A	HIS76
A	HOH364
A	HOH451

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 223

Chain	Residue
A	ASN130
A	ASP133
A	HIS166
A	HOH523

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 224

Chain	Residue
A	THR14
A	ASP50
A	GLU116
A	GTP221
A	HOH374

---

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

Chain	Residue
A	ASN25
A	GLY28
A	LYS30
A	LEU61
A	HOH310

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 226

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

---

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 227

Chain	Residue
A	LYS171
A	THR181
A	SER185
A	VAL211
A	HOH369
A	HOH413
A	HOH512

---

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NO3 A 228

Chain	Residue
A	SER5
A	ALA6
A	LYS13
A	GLY117
A	ALA118
A	GLY119
A	GLY120
A	LEU121
A	MET131
A	HOH391

---

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 229

Chain	Residue
A	LEU168
A	ASP169
A	TYR170
A	ASN200
A	HOH493

---

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

Chain	Residue
A	GLU87
A	GLU88
A	LEU217
A	HOH448
A	HOH481
A	HOH484

---

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 231

Chain	Residue
A	ASN8
A	ASN149

---

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 232

Chain	Residue
A	LYS35
A	GLU38
A	THR39
A	ALA118
A	GTP221
A	HOH492
A	HOH520

---

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

---