Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2A2Z

Crystal Structure of human deoxycytidine kinase in complex with deoxycytidine and uridine diphosphate

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	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005829	cellular_component	cytosol
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006170	biological_process	dAMP biosynthetic process
A	0006220	biological_process	pyrimidine nucleotide metabolic process
A	0008144	molecular_function	obsolete drug binding
A	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
A	0009224	biological_process	CMP biosynthetic process
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0019136	molecular_function	deoxynucleoside kinase activity
A	0032261	biological_process	purine nucleotide salvage
A	0042803	molecular_function	protein homodimerization activity
A	0043771	molecular_function	cytidine kinase activity
A	1901135	biological_process	carbohydrate derivative metabolic 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	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005829	cellular_component	cytosol
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006170	biological_process	dAMP biosynthetic process
B	0006220	biological_process	pyrimidine nucleotide metabolic process
B	0008144	molecular_function	obsolete drug binding
B	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
B	0009224	biological_process	CMP biosynthetic process
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0019136	molecular_function	deoxynucleoside kinase activity
B	0032261	biological_process	purine nucleotide salvage
B	0042803	molecular_function	protein homodimerization activity
B	0043771	molecular_function	cytidine kinase activity
B	1901135	biological_process	carbohydrate derivative metabolic 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	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005829	cellular_component	cytosol
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006170	biological_process	dAMP biosynthetic process
C	0006220	biological_process	pyrimidine nucleotide metabolic process
C	0008144	molecular_function	obsolete drug binding
C	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
C	0009224	biological_process	CMP biosynthetic process
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0019136	molecular_function	deoxynucleoside kinase activity
C	0032261	biological_process	purine nucleotide salvage
C	0042803	molecular_function	protein homodimerization activity
C	0043771	molecular_function	cytidine kinase activity
C	1901135	biological_process	carbohydrate derivative metabolic 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	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005829	cellular_component	cytosol
D	0006139	biological_process	nucleobase-containing compound metabolic process
D	0006170	biological_process	dAMP biosynthetic process
D	0006220	biological_process	pyrimidine nucleotide metabolic process
D	0008144	molecular_function	obsolete drug binding
D	0009157	biological_process	deoxyribonucleoside monophosphate biosynthetic process
D	0009224	biological_process	CMP biosynthetic process
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0019136	molecular_function	deoxynucleoside kinase activity
D	0032261	biological_process	purine nucleotide salvage
D	0042803	molecular_function	protein homodimerization activity
D	0043771	molecular_function	cytidine kinase activity
D	1901135	biological_process	carbohydrate derivative metabolic process
D	1901293	biological_process	nucleoside phosphate biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA A 261

Chain	Residue
A	ASN60
C	GLU230

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA C 261

Chain	Residue
A	GLU230
C	ASN60

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 302

Chain	Residue
A	HOH307
A	SER35
A	GLU127
A	UDP301
A	HOH305
A	HOH306

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 402

Chain	Residue
B	SER35
B	GLU127
B	UDP401
B	HOH405
B	HOH406
B	HOH407

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 502

Chain	Residue
C	SER35
C	GLU127
C	UDP501
C	HOH505
C	HOH506
C	HOH507

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 602

Chain	Residue
D	SER35
D	GLU127
D	UDP601
D	HOH605
D	HOH606
D	HOH607

site_id	AC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DCZ A 304

Chain	Residue
A	GLU53
A	TRP58
A	LEU82
A	MET85
A	TYR86
A	PHE96
A	GLN97
A	ARG128
A	ASP133
A	PHE137
A	GLU197
A	HOH312
A	HOH319

site_id	AC8
Number of Residues	14
Details	BINDING SITE FOR RESIDUE UDP A 301

Chain	Residue
A	ALA31
A	ALA32
A	GLY33
A	LYS34
A	SER35
A	THR36
A	GLU127
A	ARG188
A	ARG192
A	ASP241
A	PHE242
A	LYS243
A	MG302
A	HOH312

site_id	AC9
Number of Residues	14
Details	BINDING SITE FOR RESIDUE DCZ B 404

Chain	Residue
B	ILE30
B	GLU53
B	TRP58
B	LEU82
B	MET85
B	TYR86
B	PHE96
B	GLN97
B	ARG128
B	ASP133
B	PHE137
B	ARG194
B	GLU197
B	HOH410

site_id	BC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE UDP B 401

Chain	Residue
B	ALA31
B	GLY33
B	LYS34
B	SER35
B	THR36
B	GLU127
B	ARG188
B	LEU191
B	ARG192
B	ASP241
B	PHE242
B	LYS243
B	MG402
B	HOH410

site_id	BC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DCZ C 504

Chain	Residue
C	ILE30
C	GLU53
C	TYR86
C	PHE96
C	GLN97
C	ARG128
C	ASP133
C	PHE137
C	GLU197
C	HOH507
C	HOH510

site_id	BC3
Number of Residues	16
Details	BINDING SITE FOR RESIDUE UDP C 501

Chain	Residue
C	THR36
C	GLU127
C	ARG188
C	LEU191
C	ARG192
C	ASP241
C	PHE242
C	LYS243
C	MG502
C	HOH514
C	HOH519
C	ALA31
C	ALA32
C	GLY33
C	LYS34
C	SER35

site_id	BC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DCZ D 604

Chain	Residue
D	ILE30
D	GLU53
D	TRP58
D	TYR86
D	PHE96
D	GLN97
D	ARG128
D	ASP133
D	PHE137
D	ARG194
D	GLU197
D	HOH609

site_id	BC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UDP D 601

Chain	Residue
D	ALA31
D	ALA32
D	GLY33
D	LYS34
D	SER35
D	THR36
D	GLU127
D	ARG188
D	LEU191
D	ARG192
D	ASP241
D	PHE242
D	LYS243
D	MG602
D	HOH609

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton acceptor","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	80
Details	Binding site: {}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 2ocp

Chain	Residue	Details
A	GLU53
A	ARG128

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

Chain	Residue	Details
B	GLU53
B	ARG128

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

Chain	Residue	Details
C	GLU53
C	ARG128

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

Chain	Residue	Details
D	GLU53
D	ARG128

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