3QXH

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

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	13
Details	BINDING SITE FOR RESIDUE 8AC A 221

Chain	Residue
A	THR9
A	HOH308
A	HOH356
A	HOH493
A	HOH556
A	THR39
A	SER79
A	VAL123
A	GLY151
A	LEU152
A	ILE153
A	ASN154
A	PO4225

---

site_id	AC2
Number of Residues	23
Details	BINDING SITE FOR RESIDUE ADP A 222

Chain	Residue
A	ASN10
A	ALA11
A	GLY12
A	LYS13
A	THR14
A	THR15
A	GLU116
A	GLN167
A	ASN175
A	LYS177
A	MG223
A	MG224
A	PO4225
A	HOH335
A	HOH337
A	HOH340
A	HOH392
A	HOH503
A	HOH520
A	HOH539
A	HOH540
A	HOH558
A	HOH563

---

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

Chain	Residue
A	THR14
A	LYS35
A	ASP50
A	GLU116
A	ADP222
A	MG224
A	PO4225
A	HOH337

---

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

Chain	Residue
A	ADP222
A	MG223
A	PO4225
A	HOH307
A	HOH337
A	HOH539
A	HOH540

---

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	ADP222
A	MG223
A	MG224
A	HOH307
A	HOH337
A	HOH496
A	HOH539

---

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 226

Chain	Residue
A	ASN130
A	ASP133
A	HOH530

---

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

Chain	Residue
A	PHE72
A	TYR73
A	ARG74
A	TYR75
A	ASP89
A	HOH568
A	HOH569

---

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 228

Chain	Residue
A	VAL41
A	ASN42
A	ASP43
A	ARG74
A	HIS76
A	HOH577

---

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

Chain	Residue
A	ASN25
A	LYS30
A	LEU61
A	HOH514
A	HOH534

---

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

Chain	Residue
A	HIS0
A	MET1
A	LYS139
A	LYS141
A	SER220
A	HOH578

---

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

---