Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1UCN

X-ray structure of human nucleoside diphosphate kinase A complexed with ADP at 2 A resolution

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 A 1161

Chain	Residue
A	ALA10
A	LYS12
A	HIS51
A	TYR52
A	GLY118
A	GLY119
A	CA1162
A	HOH1226

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 1162

Chain	Residue
A	ASP121
A	ADP1160
A	PO41161
A	HOH1192
A	HOH1226
A	GLY119

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 B 2161

Chain	Residue
B	LYS12
B	HIS51
B	TYR52
B	GLY118
B	GLY119
B	HOH2236
B	HOH2261

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA B 2162

Chain	Residue
B	GLY119
B	ADP2160
B	HOH2236
B	HOH2261

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 C 3161

Chain	Residue
C	HIS51
C	TYR52
C	GLY118
C	GLY119
C	HOH3223

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA C 3162

Chain	Residue
C	ADP3160
C	HOH3223
C	HOH3224

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA C 1001

Chain	Residue
C	GLY131
C	HOH3204
C	HOH3205
C	HOH3206

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 1002

Chain	Residue
B	GLY131
B	PHE134
B	HOH2241
B	HOH2289
B	HOH2313
B	HOH2314

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ADP A 1160

Chain	Residue
A	LYS12
A	LEU55
A	TRP60
A	LEU64
A	ARG88
A	THR94
A	ARG105
A	VAL112
A	ASN115
A	ASP121
A	CA1162
A	HOH1190

site_id	BC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ADP B 2160

Chain	Residue
B	LYS12
B	LEU55
B	TRP60
B	ARG88
B	THR94
B	ARG105
B	VAL112
B	ASN115
B	CA2162
B	HOH2211
B	HOH2261

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ADP C 3160

Chain	Residue
C	LYS12
C	TRP60
C	LEU64
C	ARG88
C	THR94
C	ARG105
C	VAL112
C	ASN115
C	CA3162
C	HOH3223

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE TRS B 1003

Chain	Residue
B	GLU152
B	HOH2312
C	GLU152

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000269\|PubMed:1851158

Chain	Residue	Details
A	GLY118
B	GLY118
C	GLY118

site_id	SWS_FT_FI2
Number of Residues	18
Details	BINDING:

Chain	Residue	Details
A	LYS12
B	THR94
B	ARG105
B	ASN115
C	LYS12
C	TRP60
C	ARG88
C	THR94
C	ARG105
C	ASN115
A	TRP60
A	ARG88
A	THR94
A	ARG105
A	ASN115
B	LYS12
B	TRP60
B	ARG88

site_id	SWS_FT_FI3
Number of Residues	9
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER120
A	SER122
A	SER125
B	SER120
B	SER122
B	SER125
C	SER120
C	SER122
C	SER125

site_id	SWS_FT_FI4
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)

Chain	Residue	Details
A	LYS100
B	LYS100
C	LYS100

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	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
A	TYR52
A	LYS12

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

Chain	Residue	Details
B	TYR52
B	LYS12

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

Chain	Residue	Details
C	TYR52
C	LYS12

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