Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1KDN

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005840	cellular_component	ribosome
A	0005856	cellular_component	cytoskeleton
A	0005886	cellular_component	plasma membrane
A	0006183	biological_process	GTP biosynthetic process
A	0006187	biological_process	dGTP biosynthetic process from dGDP
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0006414	biological_process	translational elongation
A	0007186	biological_process	G protein-coupled receptor signaling pathway
A	0009117	biological_process	nucleotide metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0009617	biological_process	response to bacterium
A	0015629	cellular_component	actin cytoskeleton
A	0016301	molecular_function	kinase activity
A	0016310	biological_process	phosphorylation
A	0016740	molecular_function	transferase activity
A	0019954	biological_process	asexual reproduction
A	0030036	biological_process	actin cytoskeleton organization
A	0030141	cellular_component	secretory granule
A	0045335	cellular_component	phagocytic vesicle
A	0045920	biological_process	negative regulation of exocytosis
A	0046872	molecular_function	metal ion binding
A	0048550	biological_process	negative regulation of pinocytosis
A	0050765	biological_process	negative regulation of phagocytosis
B	0000166	molecular_function	nucleotide binding
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005840	cellular_component	ribosome
B	0005856	cellular_component	cytoskeleton
B	0005886	cellular_component	plasma membrane
B	0006183	biological_process	GTP biosynthetic process
B	0006187	biological_process	dGTP biosynthetic process from dGDP
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0006414	biological_process	translational elongation
B	0007186	biological_process	G protein-coupled receptor signaling pathway
B	0009117	biological_process	nucleotide metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0009617	biological_process	response to bacterium
B	0015629	cellular_component	actin cytoskeleton
B	0016301	molecular_function	kinase activity
B	0016310	biological_process	phosphorylation
B	0016740	molecular_function	transferase activity
B	0019954	biological_process	asexual reproduction
B	0030036	biological_process	actin cytoskeleton organization
B	0030141	cellular_component	secretory granule
B	0045335	cellular_component	phagocytic vesicle
B	0045920	biological_process	negative regulation of exocytosis
B	0046872	molecular_function	metal ion binding
B	0048550	biological_process	negative regulation of pinocytosis
B	0050765	biological_process	negative regulation of phagocytosis
C	0000166	molecular_function	nucleotide binding
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0005840	cellular_component	ribosome
C	0005856	cellular_component	cytoskeleton
C	0005886	cellular_component	plasma membrane
C	0006183	biological_process	GTP biosynthetic process
C	0006187	biological_process	dGTP biosynthetic process from dGDP
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0006414	biological_process	translational elongation
C	0007186	biological_process	G protein-coupled receptor signaling pathway
C	0009117	biological_process	nucleotide metabolic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0009617	biological_process	response to bacterium
C	0015629	cellular_component	actin cytoskeleton
C	0016301	molecular_function	kinase activity
C	0016310	biological_process	phosphorylation
C	0016740	molecular_function	transferase activity
C	0019954	biological_process	asexual reproduction
C	0030036	biological_process	actin cytoskeleton organization
C	0030141	cellular_component	secretory granule
C	0045335	cellular_component	phagocytic vesicle
C	0045920	biological_process	negative regulation of exocytosis
C	0046872	molecular_function	metal ion binding
C	0048550	biological_process	negative regulation of pinocytosis
C	0050765	biological_process	negative regulation of phagocytosis

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 156

Chain	Residue
A	AF3157
A	ADP158
A	HOH671
A	HOH690
A	HOH698

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 156

Chain	Residue
B	HOH847
B	AF3157
B	ADP158
B	HOH604
B	HOH669

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 156

Chain	Residue
C	AF3157
C	ADP158
C	HOH667
C	HOH722
C	HOH766

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AF3 A 157

Chain	Residue
A	LYS16
A	TYR56
A	ARG92
A	ARG109
A	HIS122
A	GLY123
A	MG156
A	ADP158
A	HOH671
A	HOH690

site_id	AC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ADP A 158

Chain	Residue
A	LYS16
A	HIS59
A	PHE64
A	LEU68
A	ARG92
A	THR98
A	ARG109
A	VAL116
A	ASN119
A	MG156
A	AF3157
A	HOH671
A	HOH690
A	HOH698
A	HOH728
A	HOH793

site_id	AC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AF3 B 157

Chain	Residue
B	LYS16
B	TYR56
B	ARG92
B	ARG109
B	HIS122
B	GLY123
B	MG156
B	ADP158
B	HOH604
B	HOH669

site_id	AC7
Number of Residues	17
Details	BINDING SITE FOR RESIDUE ADP B 158

Chain	Residue
A	HOH676
B	LYS16
B	TYR56
B	HIS59
B	PHE64
B	LEU68
B	ARG92
B	THR98
B	ARG109
B	VAL116
B	ASN119
B	MG156
B	AF3157
B	HOH776
B	HOH792
B	HOH826
B	HOH847

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AF3 C 157

Chain	Residue
C	LYS16
C	TYR56
C	ARG92
C	ARG109
C	HIS122
C	GLY123
C	MG156
C	ADP158
C	HOH667
C	HOH722

site_id	AC9
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ADP C 158

Chain	Residue
C	LYS16
C	HIS59
C	PHE64
C	LEU68
C	ARG92
C	THR98
C	ARG109
C	VAL116
C	ASN119
C	MG156
C	AF3157
C	HOH722
C	HOH766
C	HOH845

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN119-VAL127

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: Pros-phosphohistidine intermediate

Chain	Residue	Details
A	HIS122
B	HIS122
C	HIS122

site_id	SWS_FT_FI2
Number of Residues	18
Details	BINDING:

Chain	Residue	Details
A	LYS16
B	THR98
B	ARG109
B	ASN119
C	LYS16
C	PHE64
C	ARG92
C	THR98
C	ARG109
C	ASN119
A	PHE64
A	ARG92
A	THR98
A	ARG109
A	ASN119
B	LYS16
B	PHE64
B	ARG92

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	5
Details	M-CSA 150

Chain	Residue	Details
A	LYS16	electrostatic stabiliser, hydrogen bond donor
A	TYR56	electrostatic stabiliser, hydrogen bond donor
A	ASN119	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
A	HIS122	hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
A	GLU133	hydrogen bond acceptor, increase nucleophilicity, steric role

site_id	MCSA2
Number of Residues	5
Details	M-CSA 150

Chain	Residue	Details
B	LYS16	electrostatic stabiliser, hydrogen bond donor
B	TYR56	electrostatic stabiliser, hydrogen bond donor
B	ASN119	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
B	HIS122	hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
B	GLU133	hydrogen bond acceptor, increase nucleophilicity, steric role

site_id	MCSA3
Number of Residues	5
Details	M-CSA 150

Chain	Residue	Details
C	LYS16	electrostatic stabiliser, hydrogen bond donor
C	TYR56	electrostatic stabiliser, hydrogen bond donor
C	ASN119	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
C	HIS122	hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
C	GLU133	hydrogen bond acceptor, increase nucleophilicity, steric role

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