Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1U8W

Crystal structure of Arabidopsis thaliana nucleoside diphosphate kinase 1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000325	cellular_component	plant-type vacuole
A	0004550	molecular_function	nucleoside diphosphate 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	0005777	cellular_component	peroxisome
A	0005794	cellular_component	Golgi apparatus
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0009117	biological_process	nucleotide metabolic process
A	0009506	cellular_component	plasmodesma
A	0009507	cellular_component	chloroplast
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0042542	biological_process	response to hydrogen peroxide
A	0046872	molecular_function	metal ion binding
A	0048046	cellular_component	apoplast
A	0070301	biological_process	cellular response to hydrogen peroxide
B	0000166	molecular_function	nucleotide binding
B	0000325	cellular_component	plant-type vacuole
B	0004550	molecular_function	nucleoside diphosphate 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	0005777	cellular_component	peroxisome
B	0005794	cellular_component	Golgi apparatus
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0009117	biological_process	nucleotide metabolic process
B	0009506	cellular_component	plasmodesma
B	0009507	cellular_component	chloroplast
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0042542	biological_process	response to hydrogen peroxide
B	0046872	molecular_function	metal ion binding
B	0048046	cellular_component	apoplast
B	0070301	biological_process	cellular response to hydrogen peroxide
C	0000166	molecular_function	nucleotide binding
C	0000325	cellular_component	plant-type vacuole
C	0004550	molecular_function	nucleoside diphosphate 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	0005777	cellular_component	peroxisome
C	0005794	cellular_component	Golgi apparatus
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0009117	biological_process	nucleotide metabolic process
C	0009506	cellular_component	plasmodesma
C	0009507	cellular_component	chloroplast
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0042542	biological_process	response to hydrogen peroxide
C	0046872	molecular_function	metal ion binding
C	0048046	cellular_component	apoplast
C	0070301	biological_process	cellular response to hydrogen peroxide
D	0000166	molecular_function	nucleotide binding
D	0000325	cellular_component	plant-type vacuole
D	0004550	molecular_function	nucleoside diphosphate 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	0005777	cellular_component	peroxisome
D	0005794	cellular_component	Golgi apparatus
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
D	0009117	biological_process	nucleotide metabolic process
D	0009506	cellular_component	plasmodesma
D	0009507	cellular_component	chloroplast
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0042542	biological_process	response to hydrogen peroxide
D	0046872	molecular_function	metal ion binding
D	0048046	cellular_component	apoplast
D	0070301	biological_process	cellular response to hydrogen peroxide
E	0000166	molecular_function	nucleotide binding
E	0000325	cellular_component	plant-type vacuole
E	0004550	molecular_function	nucleoside diphosphate 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	0005777	cellular_component	peroxisome
E	0005794	cellular_component	Golgi apparatus
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
E	0009117	biological_process	nucleotide metabolic process
E	0009506	cellular_component	plasmodesma
E	0009507	cellular_component	chloroplast
E	0016301	molecular_function	kinase activity
E	0016740	molecular_function	transferase activity
E	0042542	biological_process	response to hydrogen peroxide
E	0046872	molecular_function	metal ion binding
E	0048046	cellular_component	apoplast
E	0070301	biological_process	cellular response to hydrogen peroxide
F	0000166	molecular_function	nucleotide binding
F	0000325	cellular_component	plant-type vacuole
F	0004550	molecular_function	nucleoside diphosphate 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	0005777	cellular_component	peroxisome
F	0005794	cellular_component	Golgi apparatus
F	0005829	cellular_component	cytosol
F	0005886	cellular_component	plasma membrane
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process
F	0009117	biological_process	nucleotide metabolic process
F	0009506	cellular_component	plasmodesma
F	0009507	cellular_component	chloroplast
F	0016301	molecular_function	kinase activity
F	0016740	molecular_function	transferase activity
F	0042542	biological_process	response to hydrogen peroxide
F	0046872	molecular_function	metal ion binding
F	0048046	cellular_component	apoplast
F	0070301	biological_process	cellular response to hydrogen peroxide

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN112-VAL120

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	36
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"}]}

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	ASN112
A	LYS9

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

Chain	Residue	Details
D	TYR49
D	LYS9

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

Chain	Residue	Details
E	TYR49
E	LYS9

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

Chain	Residue	Details
F	TYR49
F	LYS9

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

Chain	Residue	Details
B	ASN112
B	LYS9

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

Chain	Residue	Details
C	ASN112
C	LYS9

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

Chain	Residue	Details
D	ASN112
D	LYS9

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

Chain	Residue	Details
E	ASN112
E	LYS9

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

Chain	Residue	Details
F	ASN112
F	LYS9

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

Chain	Residue	Details
A	TYR49
A	LYS9

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

Chain	Residue	Details
B	TYR49
B	LYS9

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

Chain	Residue	Details
C	TYR49
C	LYS9

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