Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1ZMX

Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004136	molecular_function	deoxyadenosine kinase activity
A	0004137	molecular_function	deoxycytidine kinase activity
A	0004138	molecular_function	deoxyguanosine kinase activity
A	0004797	molecular_function	thymidine kinase activity
A	0004849	molecular_function	uridine kinase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006170	biological_process	dAMP biosynthetic process
A	0006222	biological_process	UMP biosynthetic process
A	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
A	0009224	biological_process	CMP biosynthetic process
A	0016301	molecular_function	kinase activity
A	0016310	biological_process	phosphorylation
A	0016740	molecular_function	transferase activity
A	0019136	molecular_function	deoxynucleoside kinase activity
A	0043174	biological_process	nucleoside salvage
A	0043771	molecular_function	cytidine kinase activity
A	0071897	biological_process	DNA biosynthetic process
A	1901293	biological_process	nucleoside phosphate biosynthetic process
B	0000166	molecular_function	nucleotide binding
B	0004136	molecular_function	deoxyadenosine kinase activity
B	0004137	molecular_function	deoxycytidine kinase activity
B	0004138	molecular_function	deoxyguanosine kinase activity
B	0004797	molecular_function	thymidine kinase activity
B	0004849	molecular_function	uridine kinase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006170	biological_process	dAMP biosynthetic process
B	0006222	biological_process	UMP biosynthetic process
B	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
B	0009224	biological_process	CMP biosynthetic process
B	0016301	molecular_function	kinase activity
B	0016310	biological_process	phosphorylation
B	0016740	molecular_function	transferase activity
B	0019136	molecular_function	deoxynucleoside kinase activity
B	0043174	biological_process	nucleoside salvage
B	0043771	molecular_function	cytidine kinase activity
B	0071897	biological_process	DNA biosynthetic process
B	1901293	biological_process	nucleoside phosphate biosynthetic process
C	0000166	molecular_function	nucleotide binding
C	0004136	molecular_function	deoxyadenosine kinase activity
C	0004137	molecular_function	deoxycytidine kinase activity
C	0004138	molecular_function	deoxyguanosine kinase activity
C	0004797	molecular_function	thymidine kinase activity
C	0004849	molecular_function	uridine kinase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006170	biological_process	dAMP biosynthetic process
C	0006222	biological_process	UMP biosynthetic process
C	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
C	0009224	biological_process	CMP biosynthetic process
C	0016301	molecular_function	kinase activity
C	0016310	biological_process	phosphorylation
C	0016740	molecular_function	transferase activity
C	0019136	molecular_function	deoxynucleoside kinase activity
C	0043174	biological_process	nucleoside salvage
C	0043771	molecular_function	cytidine kinase activity
C	0071897	biological_process	DNA biosynthetic process
C	1901293	biological_process	nucleoside phosphate biosynthetic process
D	0000166	molecular_function	nucleotide binding
D	0004136	molecular_function	deoxyadenosine kinase activity
D	0004137	molecular_function	deoxycytidine kinase activity
D	0004138	molecular_function	deoxyguanosine kinase activity
D	0004797	molecular_function	thymidine kinase activity
D	0004849	molecular_function	uridine kinase activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0006139	biological_process	nucleobase-containing compound metabolic process
D	0006170	biological_process	dAMP biosynthetic process
D	0006222	biological_process	UMP biosynthetic process
D	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
D	0009224	biological_process	CMP biosynthetic process
D	0016301	molecular_function	kinase activity
D	0016310	biological_process	phosphorylation
D	0016740	molecular_function	transferase activity
D	0019136	molecular_function	deoxynucleoside kinase activity
D	0043174	biological_process	nucleoside salvage
D	0043771	molecular_function	cytidine kinase activity
D	0071897	biological_process	DNA biosynthetic process
D	1901293	biological_process	nucleoside phosphate biosynthetic process
E	0000166	molecular_function	nucleotide binding
E	0004136	molecular_function	deoxyadenosine kinase activity
E	0004137	molecular_function	deoxycytidine kinase activity
E	0004138	molecular_function	deoxyguanosine kinase activity
E	0004797	molecular_function	thymidine kinase activity
E	0004849	molecular_function	uridine kinase activity
E	0005524	molecular_function	ATP binding
E	0005737	cellular_component	cytoplasm
E	0005739	cellular_component	mitochondrion
E	0006139	biological_process	nucleobase-containing compound metabolic process
E	0006170	biological_process	dAMP biosynthetic process
E	0006222	biological_process	UMP biosynthetic process
E	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
E	0009224	biological_process	CMP biosynthetic process
E	0016301	molecular_function	kinase activity
E	0016310	biological_process	phosphorylation
E	0016740	molecular_function	transferase activity
E	0019136	molecular_function	deoxynucleoside kinase activity
E	0043174	biological_process	nucleoside salvage
E	0043771	molecular_function	cytidine kinase activity
E	0071897	biological_process	DNA biosynthetic process
E	1901293	biological_process	nucleoside phosphate biosynthetic process
F	0000166	molecular_function	nucleotide binding
F	0004136	molecular_function	deoxyadenosine kinase activity
F	0004137	molecular_function	deoxycytidine kinase activity
F	0004138	molecular_function	deoxyguanosine kinase activity
F	0004797	molecular_function	thymidine kinase activity
F	0004849	molecular_function	uridine kinase activity
F	0005524	molecular_function	ATP binding
F	0005737	cellular_component	cytoplasm
F	0005739	cellular_component	mitochondrion
F	0006139	biological_process	nucleobase-containing compound metabolic process
F	0006170	biological_process	dAMP biosynthetic process
F	0006222	biological_process	UMP biosynthetic process
F	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
F	0009224	biological_process	CMP biosynthetic process
F	0016301	molecular_function	kinase activity
F	0016310	biological_process	phosphorylation
F	0016740	molecular_function	transferase activity
F	0019136	molecular_function	deoxynucleoside kinase activity
F	0043174	biological_process	nucleoside salvage
F	0043771	molecular_function	cytidine kinase activity
F	0071897	biological_process	DNA biosynthetic process
F	1901293	biological_process	nucleoside phosphate biosynthetic process
G	0000166	molecular_function	nucleotide binding
G	0004136	molecular_function	deoxyadenosine kinase activity
G	0004137	molecular_function	deoxycytidine kinase activity
G	0004138	molecular_function	deoxyguanosine kinase activity
G	0004797	molecular_function	thymidine kinase activity
G	0004849	molecular_function	uridine kinase activity
G	0005524	molecular_function	ATP binding
G	0005737	cellular_component	cytoplasm
G	0005739	cellular_component	mitochondrion
G	0006139	biological_process	nucleobase-containing compound metabolic process
G	0006170	biological_process	dAMP biosynthetic process
G	0006222	biological_process	UMP biosynthetic process
G	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
G	0009224	biological_process	CMP biosynthetic process
G	0016301	molecular_function	kinase activity
G	0016310	biological_process	phosphorylation
G	0016740	molecular_function	transferase activity
G	0019136	molecular_function	deoxynucleoside kinase activity
G	0043174	biological_process	nucleoside salvage
G	0043771	molecular_function	cytidine kinase activity
G	0071897	biological_process	DNA biosynthetic process
G	1901293	biological_process	nucleoside phosphate biosynthetic process
H	0000166	molecular_function	nucleotide binding
H	0004136	molecular_function	deoxyadenosine kinase activity
H	0004137	molecular_function	deoxycytidine kinase activity
H	0004138	molecular_function	deoxyguanosine kinase activity
H	0004797	molecular_function	thymidine kinase activity
H	0004849	molecular_function	uridine kinase activity
H	0005524	molecular_function	ATP binding
H	0005737	cellular_component	cytoplasm
H	0005739	cellular_component	mitochondrion
H	0006139	biological_process	nucleobase-containing compound metabolic process
H	0006170	biological_process	dAMP biosynthetic process
H	0006222	biological_process	UMP biosynthetic process
H	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
H	0009224	biological_process	CMP biosynthetic process
H	0016301	molecular_function	kinase activity
H	0016310	biological_process	phosphorylation
H	0016740	molecular_function	transferase activity
H	0019136	molecular_function	deoxynucleoside kinase activity
H	0043174	biological_process	nucleoside salvage
H	0043771	molecular_function	cytidine kinase activity
H	0071897	biological_process	DNA biosynthetic process
H	1901293	biological_process	nucleoside phosphate biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 1300

Chain	Residue
A	ASN28
A	GLY30
A	SER31
A	GLY32
A	LYS33
A	THR34
A	ARG167

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 1301

Chain	Residue
B	SER31
B	GLY32
B	LYS33
B	THR34
B	ARG167
B	ASN28
B	GLY30

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 G 1302

Chain	Residue
G	ASN28
G	GLY30
G	SER31
G	GLY32
G	LYS33
G	THR34
G	ARG167

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 H 1303

Chain	Residue
H	ILE29
H	GLY30
H	SER31
H	GLY32
H	LYS33
H	THR34

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 1304

Chain	Residue
E	ASN28
E	GLY30
E	SER31
E	GLY32
E	LYS33
E	THR34
E	ARG167

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 F 1305

Chain	Residue
F	ASN28
F	GLY30
F	SER31
F	GLY32
F	LYS33
F	THR34
F	ARG167

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 C 1306

Chain	Residue
C	ASN28
C	GLY30
C	SER31
C	GLY32
C	LYS33
C	THR34
C	ARG167

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 D 1307

Chain	Residue
D	ASN28
D	GLY30
D	SER31
D	GLY32
D	LYS33
D	THR34
D	ARG167

site_id	AC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE THM A 1400

Chain	Residue
A	ILE29
A	GLU52
A	TRP57
A	TYR70
A	PHE80
A	GLN81
A	VAL84
A	MET88
A	ARG105
A	ALA110
A	PHE114

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE THM B 1401

Chain	Residue
B	ILE29
B	GLU52
B	TRP57
B	TYR70
B	PHE80
B	GLN81
B	ARG105
B	ALA110
B	PHE114

site_id	BC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE THM G 1402

Chain	Residue
G	ILE29
G	GLU52
G	TRP57
G	TYR70
G	PHE80
G	GLN81
G	ARG105
G	ALA110
G	PHE114

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE THM H 1403

Chain	Residue
H	GLU52
H	TRP57
H	TYR70
H	PHE80
H	GLN81
H	ARG105
H	ALA110
H	PHE114

site_id	BC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE THM E 1404

Chain	Residue
E	ARG105
E	ALA110
E	PHE114
E	ILE29
E	GLU52
E	TRP57
E	TYR70
E	PHE80
E	GLN81
E	VAL84

site_id	BC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE THM F 1405

Chain	Residue
F	ILE29
F	GLU52
F	TRP57
F	TYR70
F	PHE80
F	GLN81
F	VAL84
F	ARG105
F	ALA110
F	PHE114

site_id	BC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE THM C 1406

Chain	Residue
C	ILE29
C	GLU52
C	TRP57
C	LEU66
C	TYR70
C	PHE80
C	GLN81
C	VAL84
C	ARG105
C	ALA110
C	PHE114

site_id	BC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE THM D 1407

Chain	Residue
D	ILE29
D	GLU52
D	TRP57
D	TYR70
D	PHE80
D	GLN81
D	VAL84
D	ARG105
D	ALA110
D	PHE114
D	MET118

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Proton acceptor => ECO:0000255

Chain	Residue	Details
A	GLU104
B	GLU104
C	GLU104
D	GLU104
E	GLU104
F	GLU104
G	GLU104
H	GLU104

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	GLY27
B	GLY27
C	GLY27
D	GLY27
E	GLY27
F	GLY27
G	GLY27
H	GLY27

site_id	SWS_FT_FI3
Number of Residues	40
Details	BINDING:

Chain	Residue	Details
A	GLU52
B	GLU172
C	GLU52
C	TYR70
C	GLN81
C	ARG105
C	GLU172
D	GLU52
D	TYR70
D	GLN81
D	ARG105
A	TYR70
D	GLU172
E	GLU52
E	TYR70
E	GLN81
E	ARG105
E	GLU172
F	GLU52
F	TYR70
F	GLN81
F	ARG105
A	GLN81
F	GLU172
G	GLU52
G	TYR70
G	GLN81
G	ARG105
G	GLU172
H	GLU52
H	TYR70
H	GLN81
H	ARG105
A	ARG105
H	GLU172
A	GLU172
B	GLU52
B	TYR70
B	GLN81
B	ARG105

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