Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1S5Z

NDP kinase in complex with adenosine phosphonoacetic acid

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PO4 C 1161

Chain	Residue
C	THR98
C	ARG109
C	HOH1281
C	HOH1300
C	HOH1317
C	HOH1318

site_id	AC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SON A 1160

Chain	Residue
A	LEU68
A	ARG92
A	THR98
A	ARG109
A	VAL116
A	ASN119
A	HOH1206
A	HOH1246
A	LYS16
A	HIS59
A	PHE64

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	6
Details	ACT_SITE: Pros-phosphohistidine intermediate

Chain	Residue	Details
A	HIS122
B	HIS122
C	HIS122
D	HIS122
E	HIS122
F	HIS122

site_id	SWS_FT_FI2
Number of Residues	36
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
D	LYS16
A	PHE64
D	PHE64
D	ARG92
D	THR98
D	ARG109
D	ASN119
E	LYS16
E	PHE64
E	ARG92
E	THR98
E	ARG109
A	ARG92
E	ASN119
F	LYS16
F	PHE64
F	ARG92
F	THR98
F	ARG109
F	ASN119
A	THR98
A	ARG109
A	ASN119
B	LYS16
B	PHE64
B	ARG92

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	ASN119
A	LYS16

site_id	CSA10
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
D	TYR56
D	LYS16

site_id	CSA11
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
E	TYR56
E	LYS16

site_id	CSA12
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
F	TYR56
F	LYS16

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
B	ASN119
B	LYS16

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
C	ASN119
C	LYS16

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
D	ASN119
D	LYS16

site_id	CSA5
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
E	ASN119
E	LYS16

site_id	CSA6
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
F	ASN119
F	LYS16

site_id	CSA7
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	TYR56
A	LYS16

site_id	CSA8
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
B	TYR56
B	LYS16

site_id	CSA9
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
C	TYR56
C	LYS16

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

site_id	MCSA4
Number of Residues	5
Details	M-CSA 150

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

site_id	MCSA5
Number of Residues	5
Details	M-CSA 150

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

site_id	MCSA6
Number of Residues	5
Details	M-CSA 150

Chain	Residue	Details
F	LYS16	electrostatic stabiliser, hydrogen bond donor
F	TYR56	electrostatic stabiliser, hydrogen bond donor
F	ASN119	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
F	HIS122	hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
F	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)