1JXV

Crystal Structure of Human Nucleoside Diphosphate Kinase A

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion binding
A	0003677	molecular_function	DNA binding
A	0003723	molecular_function	RNA binding
A	0004520	molecular_function	DNA endonuclease activity
A	0004536	molecular_function	DNA nuclease activity
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0004673	molecular_function	protein histidine kinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005769	cellular_component	early endosome
A	0005829	cellular_component	cytosol
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0006308	biological_process	DNA catabolic process
A	0006309	biological_process	apoptotic DNA fragmentation
A	0006720	biological_process	isoprenoid metabolic process
A	0006897	biological_process	endocytosis
A	0007399	biological_process	nervous system development
A	0007595	biological_process	lactation
A	0008285	biological_process	negative regulation of cell population proliferation
A	0008296	molecular_function	3'-5'-DNA exonuclease activity
A	0009117	biological_process	nucleotide metabolic process
A	0009132	biological_process	nucleoside diphosphate metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016020	cellular_component	membrane
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
A	0019003	molecular_function	GDP binding
A	0030154	biological_process	cell differentiation
A	0030879	biological_process	mammary gland development
A	0032587	cellular_component	ruffle membrane
A	0034214	biological_process	protein hexamerization
A	0042304	biological_process	regulation of fatty acid biosynthetic process
A	0042802	molecular_function	identical protein binding
A	0042981	biological_process	regulation of apoptotic process
A	0043024	molecular_function	ribosomal small subunit binding
A	0043531	molecular_function	ADP binding
A	0046042	biological_process	ITP biosynthetic process
A	0046356	biological_process	acetyl-CoA catabolic process
A	0046872	molecular_function	metal ion binding
A	0047887	molecular_function	farnesyl diphosphate kinase activity
A	0050679	biological_process	positive regulation of epithelial cell proliferation
A	0070062	cellular_component	extracellular exosome
A	0120225	molecular_function	coenzyme A binding
A	0120226	molecular_function	succinyl-CoA binding
A	1905502	molecular_function	acetyl-CoA binding
B	0000166	molecular_function	nucleotide binding
B	0000287	molecular_function	magnesium ion binding
B	0003677	molecular_function	DNA binding
B	0003723	molecular_function	RNA binding
B	0004520	molecular_function	DNA endonuclease activity
B	0004536	molecular_function	DNA nuclease activity
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0004673	molecular_function	protein histidine kinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005769	cellular_component	early endosome
B	0005829	cellular_component	cytosol
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0006308	biological_process	DNA catabolic process
B	0006309	biological_process	apoptotic DNA fragmentation
B	0006720	biological_process	isoprenoid metabolic process
B	0006897	biological_process	endocytosis
B	0007399	biological_process	nervous system development
B	0007595	biological_process	lactation
B	0008285	biological_process	negative regulation of cell population proliferation
B	0008296	molecular_function	3'-5'-DNA exonuclease activity
B	0009117	biological_process	nucleotide metabolic process
B	0009132	biological_process	nucleoside diphosphate metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016020	cellular_component	membrane
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
B	0019003	molecular_function	GDP binding
B	0030154	biological_process	cell differentiation
B	0030879	biological_process	mammary gland development
B	0032587	cellular_component	ruffle membrane
B	0034214	biological_process	protein hexamerization
B	0042304	biological_process	regulation of fatty acid biosynthetic process
B	0042802	molecular_function	identical protein binding
B	0042981	biological_process	regulation of apoptotic process
B	0043024	molecular_function	ribosomal small subunit binding
B	0043531	molecular_function	ADP binding
B	0046042	biological_process	ITP biosynthetic process
B	0046356	biological_process	acetyl-CoA catabolic process
B	0046872	molecular_function	metal ion binding
B	0047887	molecular_function	farnesyl diphosphate kinase activity
B	0050679	biological_process	positive regulation of epithelial cell proliferation
B	0070062	cellular_component	extracellular exosome
B	0120225	molecular_function	coenzyme A binding
B	0120226	molecular_function	succinyl-CoA binding
B	1905502	molecular_function	acetyl-CoA binding
C	0000166	molecular_function	nucleotide binding
C	0000287	molecular_function	magnesium ion binding
C	0003677	molecular_function	DNA binding
C	0003723	molecular_function	RNA binding
C	0004520	molecular_function	DNA endonuclease activity
C	0004536	molecular_function	DNA nuclease activity
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0004673	molecular_function	protein histidine kinase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005769	cellular_component	early endosome
C	0005829	cellular_component	cytosol
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0006308	biological_process	DNA catabolic process
C	0006309	biological_process	apoptotic DNA fragmentation
C	0006720	biological_process	isoprenoid metabolic process
C	0006897	biological_process	endocytosis
C	0007399	biological_process	nervous system development
C	0007595	biological_process	lactation
C	0008285	biological_process	negative regulation of cell population proliferation
C	0008296	molecular_function	3'-5'-DNA exonuclease activity
C	0009117	biological_process	nucleotide metabolic process
C	0009132	biological_process	nucleoside diphosphate metabolic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0016020	cellular_component	membrane
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
C	0019003	molecular_function	GDP binding
C	0030154	biological_process	cell differentiation
C	0030879	biological_process	mammary gland development
C	0032587	cellular_component	ruffle membrane
C	0034214	biological_process	protein hexamerization
C	0042304	biological_process	regulation of fatty acid biosynthetic process
C	0042802	molecular_function	identical protein binding
C	0042981	biological_process	regulation of apoptotic process
C	0043024	molecular_function	ribosomal small subunit binding
C	0043531	molecular_function	ADP binding
C	0046042	biological_process	ITP biosynthetic process
C	0046356	biological_process	acetyl-CoA catabolic process
C	0046872	molecular_function	metal ion binding
C	0047887	molecular_function	farnesyl diphosphate kinase activity
C	0050679	biological_process	positive regulation of epithelial cell proliferation
C	0070062	cellular_component	extracellular exosome
C	0120225	molecular_function	coenzyme A binding
C	0120226	molecular_function	succinyl-CoA binding
C	1905502	molecular_function	acetyl-CoA binding
D	0000166	molecular_function	nucleotide binding
D	0000287	molecular_function	magnesium ion binding
D	0003677	molecular_function	DNA binding
D	0003723	molecular_function	RNA binding
D	0004520	molecular_function	DNA endonuclease activity
D	0004536	molecular_function	DNA nuclease activity
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0004673	molecular_function	protein histidine kinase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005769	cellular_component	early endosome
D	0005829	cellular_component	cytosol
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
D	0006308	biological_process	DNA catabolic process
D	0006309	biological_process	apoptotic DNA fragmentation
D	0006720	biological_process	isoprenoid metabolic process
D	0006897	biological_process	endocytosis
D	0007399	biological_process	nervous system development
D	0007595	biological_process	lactation
D	0008285	biological_process	negative regulation of cell population proliferation
D	0008296	molecular_function	3'-5'-DNA exonuclease activity
D	0009117	biological_process	nucleotide metabolic process
D	0009132	biological_process	nucleoside diphosphate metabolic process
D	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016020	cellular_component	membrane
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
D	0019003	molecular_function	GDP binding
D	0030154	biological_process	cell differentiation
D	0030879	biological_process	mammary gland development
D	0032587	cellular_component	ruffle membrane
D	0034214	biological_process	protein hexamerization
D	0042304	biological_process	regulation of fatty acid biosynthetic process
D	0042802	molecular_function	identical protein binding
D	0042981	biological_process	regulation of apoptotic process
D	0043024	molecular_function	ribosomal small subunit binding
D	0043531	molecular_function	ADP binding
D	0046042	biological_process	ITP biosynthetic process
D	0046356	biological_process	acetyl-CoA catabolic process
D	0046872	molecular_function	metal ion binding
D	0047887	molecular_function	farnesyl diphosphate kinase activity
D	0050679	biological_process	positive regulation of epithelial cell proliferation
D	0070062	cellular_component	extracellular exosome
D	0120225	molecular_function	coenzyme A binding
D	0120226	molecular_function	succinyl-CoA binding
D	1905502	molecular_function	acetyl-CoA binding
E	0000166	molecular_function	nucleotide binding
E	0000287	molecular_function	magnesium ion binding
E	0003677	molecular_function	DNA binding
E	0003723	molecular_function	RNA binding
E	0004520	molecular_function	DNA endonuclease activity
E	0004536	molecular_function	DNA nuclease activity
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0004673	molecular_function	protein histidine kinase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005769	cellular_component	early endosome
E	0005829	cellular_component	cytosol
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
E	0006308	biological_process	DNA catabolic process
E	0006309	biological_process	apoptotic DNA fragmentation
E	0006720	biological_process	isoprenoid metabolic process
E	0006897	biological_process	endocytosis
E	0007399	biological_process	nervous system development
E	0007595	biological_process	lactation
E	0008285	biological_process	negative regulation of cell population proliferation
E	0008296	molecular_function	3'-5'-DNA exonuclease activity
E	0009117	biological_process	nucleotide metabolic process
E	0009132	biological_process	nucleoside diphosphate metabolic process
E	0009142	biological_process	nucleoside triphosphate biosynthetic process
E	0016020	cellular_component	membrane
E	0016301	molecular_function	kinase activity
E	0016740	molecular_function	transferase activity
E	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
E	0019003	molecular_function	GDP binding
E	0030154	biological_process	cell differentiation
E	0030879	biological_process	mammary gland development
E	0032587	cellular_component	ruffle membrane
E	0034214	biological_process	protein hexamerization
E	0042304	biological_process	regulation of fatty acid biosynthetic process
E	0042802	molecular_function	identical protein binding
E	0042981	biological_process	regulation of apoptotic process
E	0043024	molecular_function	ribosomal small subunit binding
E	0043531	molecular_function	ADP binding
E	0046042	biological_process	ITP biosynthetic process
E	0046356	biological_process	acetyl-CoA catabolic process
E	0046872	molecular_function	metal ion binding
E	0047887	molecular_function	farnesyl diphosphate kinase activity
E	0050679	biological_process	positive regulation of epithelial cell proliferation
E	0070062	cellular_component	extracellular exosome
E	0120225	molecular_function	coenzyme A binding
E	0120226	molecular_function	succinyl-CoA binding
E	1905502	molecular_function	acetyl-CoA binding
F	0000166	molecular_function	nucleotide binding
F	0000287	molecular_function	magnesium ion binding
F	0003677	molecular_function	DNA binding
F	0003723	molecular_function	RNA binding
F	0004520	molecular_function	DNA endonuclease activity
F	0004536	molecular_function	DNA nuclease activity
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0004673	molecular_function	protein histidine kinase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005769	cellular_component	early endosome
F	0005829	cellular_component	cytosol
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process
F	0006308	biological_process	DNA catabolic process
F	0006309	biological_process	apoptotic DNA fragmentation
F	0006720	biological_process	isoprenoid metabolic process
F	0006897	biological_process	endocytosis
F	0007399	biological_process	nervous system development
F	0007595	biological_process	lactation
F	0008285	biological_process	negative regulation of cell population proliferation
F	0008296	molecular_function	3'-5'-DNA exonuclease activity
F	0009117	biological_process	nucleotide metabolic process
F	0009132	biological_process	nucleoside diphosphate metabolic process
F	0009142	biological_process	nucleoside triphosphate biosynthetic process
F	0016020	cellular_component	membrane
F	0016301	molecular_function	kinase activity
F	0016740	molecular_function	transferase activity
F	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
F	0019003	molecular_function	GDP binding
F	0030154	biological_process	cell differentiation
F	0030879	biological_process	mammary gland development
F	0032587	cellular_component	ruffle membrane
F	0034214	biological_process	protein hexamerization
F	0042304	biological_process	regulation of fatty acid biosynthetic process
F	0042802	molecular_function	identical protein binding
F	0042981	biological_process	regulation of apoptotic process
F	0043024	molecular_function	ribosomal small subunit binding
F	0043531	molecular_function	ADP binding
F	0046042	biological_process	ITP biosynthetic process
F	0046356	biological_process	acetyl-CoA catabolic process
F	0046872	molecular_function	metal ion binding
F	0047887	molecular_function	farnesyl diphosphate kinase activity
F	0050679	biological_process	positive regulation of epithelial cell proliferation
F	0070062	cellular_component	extracellular exosome
F	0120225	molecular_function	coenzyme A binding
F	0120226	molecular_function	succinyl-CoA binding
F	1905502	molecular_function	acetyl-CoA binding

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	ASN115-VAL123

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"source":"PubMed","id":"1851158","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	36
Details	Binding site: {}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	18
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	12
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)"}

Chain

Residue

Details

---

Catalytic Information from CSA

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

Chain	Residue	Details
A	ASN115
A	LYS12

---

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

Chain	Residue	Details
D	TYR52
D	LYS12

---

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

Chain	Residue	Details
E	TYR52
E	LYS12

---

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

Chain	Residue	Details
F	TYR52
F	LYS12

---

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

Chain	Residue	Details
B	ASN115
B	LYS12

---

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

Chain	Residue	Details
C	ASN115
C	LYS12

---

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

Chain	Residue	Details
D	ASN115
D	LYS12

---

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

Chain	Residue	Details
E	ASN115
E	LYS12

---

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

Chain	Residue	Details
F	ASN115
F	LYS12

---

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

Chain	Residue	Details
A	TYR52
A	LYS12

---

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

Chain	Residue	Details
B	TYR52
B	LYS12

---

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

Chain	Residue	Details
C	TYR52
C	LYS12

---