Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

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
A	0009117	biological_process	nucleotide metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016301	molecular_function	kinase activity
A	0046872	molecular_function	metal ion binding
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
B	0009117	biological_process	nucleotide metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016301	molecular_function	kinase activity
B	0046872	molecular_function	metal ion binding
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
C	0009117	biological_process	nucleotide metabolic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0016301	molecular_function	kinase activity
C	0046872	molecular_function	metal ion binding
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
D	0009117	biological_process	nucleotide metabolic process
D	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016301	molecular_function	kinase activity
D	0046872	molecular_function	metal ion binding
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
E	0009117	biological_process	nucleotide metabolic process
E	0009142	biological_process	nucleoside triphosphate biosynthetic process
E	0016301	molecular_function	kinase activity
E	0046872	molecular_function	metal ion binding
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
F	0009117	biological_process	nucleotide metabolic process
F	0009142	biological_process	nucleoside triphosphate biosynthetic process
F	0016301	molecular_function	kinase activity
F	0046872	molecular_function	metal ion binding
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
G	0009117	biological_process	nucleotide metabolic process
G	0009142	biological_process	nucleoside triphosphate biosynthetic process
G	0016301	molecular_function	kinase activity
G	0046872	molecular_function	metal ion binding
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
H	0009117	biological_process	nucleotide metabolic process
H	0009142	biological_process	nucleoside triphosphate biosynthetic process
H	0016301	molecular_function	kinase activity
H	0046872	molecular_function	metal ion binding

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	ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255\|HAMAP-Rule:MF_00451

Chain	Residue	Details
A	HIS115
B	HIS115
C	HIS115
D	HIS115
E	HIS115
F	HIS115
G	HIS115
H	HIS115

site_id	SWS_FT_FI2
Number of Residues	48
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00451

Chain	Residue	Details
A	LYS9
B	THR91
B	ARG102
B	ASN112
C	LYS9
C	PHE57
C	ARG85
C	THR91
C	ARG102
C	ASN112
D	LYS9
A	PHE57
D	PHE57
D	ARG85
D	THR91
D	ARG102
D	ASN112
E	LYS9
E	PHE57
E	ARG85
E	THR91
E	ARG102
A	ARG85
E	ASN112
F	LYS9
F	PHE57
F	ARG85
F	THR91
F	ARG102
F	ASN112
G	LYS9
G	PHE57
G	ARG85
A	THR91
G	THR91
G	ARG102
G	ASN112
H	LYS9
H	PHE57
H	ARG85
H	THR91
H	ARG102
H	ASN112
A	ARG102
A	ASN112
B	LYS9
B	PHE57
B	ARG85

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)