3Q8Y

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP and Vanadate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0005524	molecular_function	ATP binding
E	0005737	cellular_component	cytoplasm
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0005524	molecular_function	ATP binding
F	0005737	cellular_component	cytoplasm
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process
G	0004550	molecular_function	nucleoside diphosphate kinase activity
G	0005524	molecular_function	ATP binding
G	0005737	cellular_component	cytoplasm
G	0006183	biological_process	GTP biosynthetic process
G	0006228	biological_process	UTP biosynthetic process
G	0006241	biological_process	CTP biosynthetic process
H	0004550	molecular_function	nucleoside diphosphate kinase activity
H	0005524	molecular_function	ATP binding
H	0005737	cellular_component	cytoplasm
H	0006183	biological_process	GTP biosynthetic process
H	0006228	biological_process	UTP biosynthetic process
H	0006241	biological_process	CTP biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ADP A 158

Chain	Residue
A	LYS9
A	HIS52
A	PHE57
A	THR91
A	VAL109
A	GLY110
A	ASN112
A	ASP118
A	VO4159

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE VO4 A 159

Chain	Residue
A	LYS9
A	TYR49
A	ARG102
A	HIS115
A	GLY116
A	ADP158

---

site_id	AC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ADP B 158

Chain	Residue
B	GLU51
B	HIS52
B	PHE57
B	VAL109
B	GLY110
B	ASP118
B	VO4159
B	MG160
B	HOH181

---

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE VO4 B 159

Chain	Residue
B	LYS9
B	TYR49
B	ARG102
B	HIS115
B	GLY116
B	ADP158

---

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG B 160

Chain	Residue
B	ADP158
B	HOH181

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE VO4 C 158

Chain	Residue
C	LYS9
C	TYR49
C	ARG102
C	HIS115
C	GLY116

---

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ADP D 158

Chain	Residue
D	GLU51
D	HIS52
D	PHE57
D	VAL109
D	HIS115
D	ASP118
D	VO4159
D	MG160

---

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE VO4 D 159

Chain	Residue
D	LYS9
D	TYR49
D	HIS115
D	GLY116
D	ADP158

---

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 160

Chain	Residue
D	GLU51
D	ASP118
D	ADP158
D	HOH168
H	HOH171

---

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ADP E 158

Chain	Residue
E	LYS9
E	HIS52
E	PHE57
E	THR91
E	VAL109
E	ASN112
E	VO4159
E	MG160

---

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE VO4 E 159

Chain	Residue
E	LYS9
E	TYR49
E	ARG102
E	HIS115
E	GLY116
E	ADP158

---

site_id	BC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG E 160

Chain	Residue
E	ADP158

---

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE VO4 F 158

Chain	Residue
F	LYS9
F	HIS48
F	TYR49
F	HIS115
F	GLY116
F	HOH168

---

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ADP G 158

Chain	Residue
G	LYS9
G	TYR49
G	HIS52
G	PHE57
G	LEU61
G	THR91
G	GLY110
G	VO4159

---

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE VO4 G 159

Chain	Residue
G	LYS9
G	TYR49
G	HIS115
G	GLY116
G	ADP158

---

site_id	BC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ADP H 158

Chain	Residue
H	LYS9
H	HIS52
H	PHE57
H	THR91
H	VAL109
H	GLY110
H	ASN112
H	VO4159
H	MG160
H	HOH172

---

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE VO4 H 159

Chain	Residue
H	LYS9
H	TYR49
H	ARG102
H	HIS115
H	GLY116
H	ADP158

---

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG H 160

Chain	Residue
H	ASP118
H	ADP158
H	HOH182

---

Functional Information from PROSITE/UniProt

site_id	PS00469
Number of Residues	9
Details	NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NiiHGSDSL

Chain	Residue	Details
A	ASN112-LEU120

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"source":"HAMAP-Rule","id":"MF_00451","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	48
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00451","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---