Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1JXV

Crystal Structure of Human Nucleoside Diphosphate Kinase A

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003723	molecular_function	RNA binding
A	0004536	molecular_function	DNA nuclease activity
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005525	molecular_function	GTP 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	0006259	biological_process	DNA 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	0008408	molecular_function	3'-5' exonuclease activity
A	0009117	biological_process	nucleotide metabolic process
A	0016020	cellular_component	membrane
A	0016301	molecular_function	kinase activity
A	0030154	biological_process	cell differentiation
A	0030879	biological_process	mammary gland development
A	0032587	cellular_component	ruffle membrane
A	0042802	molecular_function	identical protein binding
A	0042981	biological_process	regulation of apoptotic process
A	0043024	molecular_function	ribosomal small subunit binding
A	0043388	biological_process	positive regulation of DNA binding
A	0046872	molecular_function	metal ion binding
A	0050679	biological_process	positive regulation of epithelial cell proliferation
A	0070062	cellular_component	extracellular exosome
B	0000287	molecular_function	magnesium ion binding
B	0003723	molecular_function	RNA binding
B	0004536	molecular_function	DNA nuclease activity
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005525	molecular_function	GTP 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	0006259	biological_process	DNA 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	0008408	molecular_function	3'-5' exonuclease activity
B	0009117	biological_process	nucleotide metabolic process
B	0016020	cellular_component	membrane
B	0016301	molecular_function	kinase activity
B	0030154	biological_process	cell differentiation
B	0030879	biological_process	mammary gland development
B	0032587	cellular_component	ruffle membrane
B	0042802	molecular_function	identical protein binding
B	0042981	biological_process	regulation of apoptotic process
B	0043024	molecular_function	ribosomal small subunit binding
B	0043388	biological_process	positive regulation of DNA binding
B	0046872	molecular_function	metal ion binding
B	0050679	biological_process	positive regulation of epithelial cell proliferation
B	0070062	cellular_component	extracellular exosome
C	0000287	molecular_function	magnesium ion binding
C	0003723	molecular_function	RNA binding
C	0004536	molecular_function	DNA nuclease activity
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005525	molecular_function	GTP 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	0006259	biological_process	DNA 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	0008408	molecular_function	3'-5' exonuclease activity
C	0009117	biological_process	nucleotide metabolic process
C	0016020	cellular_component	membrane
C	0016301	molecular_function	kinase activity
C	0030154	biological_process	cell differentiation
C	0030879	biological_process	mammary gland development
C	0032587	cellular_component	ruffle membrane
C	0042802	molecular_function	identical protein binding
C	0042981	biological_process	regulation of apoptotic process
C	0043024	molecular_function	ribosomal small subunit binding
C	0043388	biological_process	positive regulation of DNA binding
C	0046872	molecular_function	metal ion binding
C	0050679	biological_process	positive regulation of epithelial cell proliferation
C	0070062	cellular_component	extracellular exosome
D	0000287	molecular_function	magnesium ion binding
D	0003723	molecular_function	RNA binding
D	0004536	molecular_function	DNA nuclease activity
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005525	molecular_function	GTP 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	0006259	biological_process	DNA 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	0008408	molecular_function	3'-5' exonuclease activity
D	0009117	biological_process	nucleotide metabolic process
D	0016020	cellular_component	membrane
D	0016301	molecular_function	kinase activity
D	0030154	biological_process	cell differentiation
D	0030879	biological_process	mammary gland development
D	0032587	cellular_component	ruffle membrane
D	0042802	molecular_function	identical protein binding
D	0042981	biological_process	regulation of apoptotic process
D	0043024	molecular_function	ribosomal small subunit binding
D	0043388	biological_process	positive regulation of DNA binding
D	0046872	molecular_function	metal ion binding
D	0050679	biological_process	positive regulation of epithelial cell proliferation
D	0070062	cellular_component	extracellular exosome
E	0000287	molecular_function	magnesium ion binding
E	0003723	molecular_function	RNA binding
E	0004536	molecular_function	DNA nuclease activity
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005525	molecular_function	GTP 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	0006259	biological_process	DNA 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	0008408	molecular_function	3'-5' exonuclease activity
E	0009117	biological_process	nucleotide metabolic process
E	0016020	cellular_component	membrane
E	0016301	molecular_function	kinase activity
E	0030154	biological_process	cell differentiation
E	0030879	biological_process	mammary gland development
E	0032587	cellular_component	ruffle membrane
E	0042802	molecular_function	identical protein binding
E	0042981	biological_process	regulation of apoptotic process
E	0043024	molecular_function	ribosomal small subunit binding
E	0043388	biological_process	positive regulation of DNA binding
E	0046872	molecular_function	metal ion binding
E	0050679	biological_process	positive regulation of epithelial cell proliferation
E	0070062	cellular_component	extracellular exosome
F	0000287	molecular_function	magnesium ion binding
F	0003723	molecular_function	RNA binding
F	0004536	molecular_function	DNA nuclease activity
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005525	molecular_function	GTP 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	0006259	biological_process	DNA 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	0008408	molecular_function	3'-5' exonuclease activity
F	0009117	biological_process	nucleotide metabolic process
F	0016020	cellular_component	membrane
F	0016301	molecular_function	kinase activity
F	0030154	biological_process	cell differentiation
F	0030879	biological_process	mammary gland development
F	0032587	cellular_component	ruffle membrane
F	0042802	molecular_function	identical protein binding
F	0042981	biological_process	regulation of apoptotic process
F	0043024	molecular_function	ribosomal small subunit binding
F	0043388	biological_process	positive regulation of DNA binding
F	0046872	molecular_function	metal ion binding
F	0050679	biological_process	positive regulation of epithelial cell proliferation
F	0070062	cellular_component	extracellular exosome

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	ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000269\|PubMed:1851158

Chain	Residue	Details
A	HIS118
B	HIS118
C	HIS118
D	HIS118
E	HIS118
F	HIS118

site_id	SWS_FT_FI2
Number of Residues	36
Details	BINDING:

Chain	Residue	Details
A	LYS12
B	THR94
B	ARG105
B	ASN115
C	LYS12
C	PHE60
C	ARG88
C	THR94
C	ARG105
C	ASN115
D	LYS12
A	PHE60
D	PHE60
D	ARG88
D	THR94
D	ARG105
D	ASN115
E	LYS12
E	PHE60
E	ARG88
E	THR94
E	ARG105
A	ARG88
E	ASN115
F	LYS12
F	PHE60
F	ARG88
F	THR94
F	ARG105
F	ASN115
A	THR94
A	ARG105
A	ASN115
B	LYS12
B	PHE60
B	ARG88

site_id	SWS_FT_FI3
Number of Residues	18
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER120
D	SER120
D	SER122
D	SER125
E	SER120
E	SER122
E	SER125
F	SER120
F	SER122
F	SER125
A	SER122
A	SER125
B	SER120
B	SER122
B	SER125
C	SER120
C	SER122
C	SER125

site_id	SWS_FT_FI4
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)

Chain	Residue	Details
A	LYS100
F	LYS100
B	LYS100
C	LYS100
D	LYS100
E	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	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

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