3QXX

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP and 8-aminocaprylic acid

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	13
Details	BINDING SITE FOR RESIDUE 8AC A 221

Chain	Residue
A	THR9
A	HOH252
A	HOH291
A	HOH293
A	HOH377
A	THR39
A	SER79
A	VAL123
A	GLY151
A	LEU152
A	ILE153
A	ASN154
A	PO4225

---

site_id	AC2
Number of Residues	20
Details	BINDING SITE FOR RESIDUE GDP A 222

Chain	Residue
A	ASN10
A	ALA11
A	GLY12
A	LYS13
A	THR14
A	THR15
A	GLU116
A	ASN175
A	LYS177
A	GLY178
A	MG223
A	MG224
A	PO4225
A	HOH261
A	HOH269
A	HOH290
A	HOH303
A	HOH413
A	HOH517
A	HOH534

---

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG A 223

Chain	Residue
A	GDP222
A	MG224
A	PO4225
A	HOH269
A	HOH289
A	HOH290
A	HOH517

---

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MG A 224

Chain	Residue
A	THR14
A	LYS35
A	ASP50
A	GLU116
A	GDP222
A	MG223
A	PO4225
A	HOH517

---

site_id	AC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PO4 A 225

Chain	Residue
A	THR9
A	LYS13
A	LYS35
A	ASP50
A	GLU116
A	ALA118
A	GLY119
A	8AC221
A	GDP222
A	MG223
A	MG224
A	HOH255
A	HOH289
A	HOH290
A	HOH493

---

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 226

Chain	Residue
A	ASN42
A	ASP43
A	ARG74
A	HIS76

---

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	5
Details	BINDING SITE FOR RESIDUE EDO A 228

Chain	Residue
A	LYS171
A	ASN200
A	PRO201
A	HOH474
A	HOH511

---

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 229

Chain	Residue
A	PHE72
A	TYR73
A	ARG74
A	TYR75
A	ASP89
A	HOH314
A	HOH555

---

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 230

Chain	Residue
A	GLN22
A	ASP57
A	HOH557

---

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 231

Chain	Residue
A	TYR73
A	ALA92
A	PRO93

---

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 232

Chain	Residue
A	ASN130
A	ASP133
A	HIS166
A	HOH285
A	HOH397

---

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

---