Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1ZS6

structure of human nucleoside-diphosphate kinase 3

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005741	cellular_component	mitochondrial outer membrane
A	0005829	cellular_component	cytosol
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006235	biological_process	dTTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0006281	biological_process	DNA repair
A	0006915	biological_process	apoptotic process
A	0008053	biological_process	mitochondrial fusion
A	0009117	biological_process	nucleotide metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0019003	molecular_function	GDP binding
A	0030552	molecular_function	cAMP binding
A	0034214	biological_process	protein hexamerization
A	0036064	cellular_component	ciliary basal body
A	0043531	molecular_function	ADP binding
A	0046872	molecular_function	metal ion binding
A	0070300	molecular_function	phosphatidic acid binding
A	0160204	molecular_function	mitochondrion-mitochondrion outer membrane tether activity
A	1990626	biological_process	mitochondrial outer membrane fusion
B	0000166	molecular_function	nucleotide binding
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005741	cellular_component	mitochondrial outer membrane
B	0005829	cellular_component	cytosol
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006235	biological_process	dTTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0006281	biological_process	DNA repair
B	0006915	biological_process	apoptotic process
B	0008053	biological_process	mitochondrial fusion
B	0009117	biological_process	nucleotide metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0019003	molecular_function	GDP binding
B	0030552	molecular_function	cAMP binding
B	0034214	biological_process	protein hexamerization
B	0036064	cellular_component	ciliary basal body
B	0043531	molecular_function	ADP binding
B	0046872	molecular_function	metal ion binding
B	0070300	molecular_function	phosphatidic acid binding
B	0160204	molecular_function	mitochondrion-mitochondrion outer membrane tether activity
B	1990626	biological_process	mitochondrial outer membrane fusion
D	0000166	molecular_function	nucleotide binding
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005741	cellular_component	mitochondrial outer membrane
D	0005829	cellular_component	cytosol
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006235	biological_process	dTTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
D	0006281	biological_process	DNA repair
D	0006915	biological_process	apoptotic process
D	0008053	biological_process	mitochondrial fusion
D	0009117	biological_process	nucleotide metabolic process
D	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0019003	molecular_function	GDP binding
D	0030552	molecular_function	cAMP binding
D	0034214	biological_process	protein hexamerization
D	0036064	cellular_component	ciliary basal body
D	0043531	molecular_function	ADP binding
D	0046872	molecular_function	metal ion binding
D	0070300	molecular_function	phosphatidic acid binding
D	0160204	molecular_function	mitochondrion-mitochondrion outer membrane tether activity
D	1990626	biological_process	mitochondrial outer membrane fusion

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ADP A 201

Chain	Residue
A	LYS29
A	PHE77
A	LEU81
A	ARG105
A	THR111
A	ARG122
A	VAL129
A	ASN132

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ADP B 202

Chain	Residue
B	LYS29
B	TYR69
B	LEU72
B	PHE77
B	LEU81
B	ARG105
B	THR111
B	VAL129
B	GLY130
B	ASN132
B	HOH301
D	LYS83
A	GLU169

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ADP D 203

Chain	Residue
D	LYS29
D	TYR69
D	LEU72
D	PHE77
D	LEU81
D	ARG105
D	THR111
D	ARG122
D	VAL129
D	ASN132
D	HOH307
D	HOH321

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN132-VAL140

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	Active site: {"description":"Pros-phosphohistidine intermediatee","evidences":[{"source":"PubMed","id":"39337255","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	15
Details	Binding site: {"evidences":[{"source":"PubMed","id":"39337255","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8QW2","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"39337255","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8QVZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"39337255","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8QW1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"39337255","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8QW0","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	LYS29
A	ASN132

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

Chain	Residue	Details
B	LYS29
B	ASN132

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

Chain	Residue	Details
D	LYS29
D	ASN132

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

Chain	Residue	Details
A	TYR69
A	LYS29

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

Chain	Residue	Details
B	TYR69
B	LYS29

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

Chain	Residue	Details
D	TYR69
D	LYS29

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