Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3TMK

CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0004798	molecular_function	thymidylate 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	0006227	biological_process	dUDP biosynthetic process
A	0006233	biological_process	dTDP biosynthetic process
A	0006235	biological_process	dTTP biosynthetic process
A	0009041	molecular_function	UMP/dUMP kinase activity
A	0009165	biological_process	nucleotide biosynthetic process
A	0016301	molecular_function	kinase activity
A	0046940	biological_process	nucleoside monophosphate phosphorylation
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0004798	molecular_function	thymidylate 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	0006227	biological_process	dUDP biosynthetic process
B	0006233	biological_process	dTDP biosynthetic process
B	0006235	biological_process	dTTP biosynthetic process
B	0009041	molecular_function	UMP/dUMP kinase activity
B	0009165	biological_process	nucleotide biosynthetic process
B	0016301	molecular_function	kinase activity
B	0046940	biological_process	nucleoside monophosphate phosphorylation
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0004798	molecular_function	thymidylate 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	0006227	biological_process	dUDP biosynthetic process
C	0006233	biological_process	dTDP biosynthetic process
C	0006235	biological_process	dTTP biosynthetic process
C	0009041	molecular_function	UMP/dUMP kinase activity
C	0009165	biological_process	nucleotide biosynthetic process
C	0016301	molecular_function	kinase activity
C	0046940	biological_process	nucleoside monophosphate phosphorylation
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0004798	molecular_function	thymidylate 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	0006227	biological_process	dUDP biosynthetic process
D	0006233	biological_process	dTDP biosynthetic process
D	0006235	biological_process	dTTP biosynthetic process
D	0009041	molecular_function	UMP/dUMP kinase activity
D	0009165	biological_process	nucleotide biosynthetic process
D	0016301	molecular_function	kinase activity
D	0046940	biological_process	nucleoside monophosphate phosphorylation
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0004798	molecular_function	thymidylate 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	0006227	biological_process	dUDP biosynthetic process
E	0006233	biological_process	dTDP biosynthetic process
E	0006235	biological_process	dTTP biosynthetic process
E	0009041	molecular_function	UMP/dUMP kinase activity
E	0009165	biological_process	nucleotide biosynthetic process
E	0016301	molecular_function	kinase activity
E	0046940	biological_process	nucleoside monophosphate phosphorylation
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0004798	molecular_function	thymidylate 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	0006227	biological_process	dUDP biosynthetic process
F	0006233	biological_process	dTDP biosynthetic process
F	0006235	biological_process	dTTP biosynthetic process
F	0009041	molecular_function	UMP/dUMP kinase activity
F	0009165	biological_process	nucleotide biosynthetic process
F	0016301	molecular_function	kinase activity
F	0046940	biological_process	nucleoside monophosphate phosphorylation
G	0004550	molecular_function	nucleoside diphosphate kinase activity
G	0004798	molecular_function	thymidylate kinase activity
G	0005515	molecular_function	protein binding
G	0005524	molecular_function	ATP binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0006227	biological_process	dUDP biosynthetic process
G	0006233	biological_process	dTDP biosynthetic process
G	0006235	biological_process	dTTP biosynthetic process
G	0009041	molecular_function	UMP/dUMP kinase activity
G	0009165	biological_process	nucleotide biosynthetic process
G	0016301	molecular_function	kinase activity
G	0046940	biological_process	nucleoside monophosphate phosphorylation
H	0004550	molecular_function	nucleoside diphosphate kinase activity
H	0004798	molecular_function	thymidylate kinase activity
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005737	cellular_component	cytoplasm
H	0006227	biological_process	dUDP biosynthetic process
H	0006233	biological_process	dTDP biosynthetic process
H	0006235	biological_process	dTTP biosynthetic process
H	0009041	molecular_function	UMP/dUMP kinase activity
H	0009165	biological_process	nucleotide biosynthetic process
H	0016301	molecular_function	kinase activity
H	0046940	biological_process	nucleoside monophosphate phosphorylation

Functional Information from PDB Data

site_id	AC1
Number of Residues	36
Details	BINDING SITE FOR RESIDUE T5A A 217

Chain	Residue
A	ASP14
A	PRO39
A	ARG41
A	LEU53
A	PHE69
A	ARG73
A	ARG94
A	GLY99
A	TYR102
A	GLU142
A	LYS143
A	ARG15
A	SER144
A	GLU149
A	TYR151
A	LYS187
A	GLY188
A	ILE189
A	HOH4063
A	HOH4064
A	HOH4067
A	HOH4069
A	THR16
A	HOH4070
A	HOH4071
A	HOH4084
A	HOH4438
A	HOH4454
A	HOH4499
A	HOH4554
A	GLY17
A	LYS18
A	THR19
A	THR20
A	LYS37
A	PHE38

site_id	AC2
Number of Residues	34
Details	BINDING SITE FOR RESIDUE T5A B 217

Chain	Residue
B	ASP14
B	ARG15
B	THR16
B	GLY17
B	LYS18
B	THR19
B	THR20
B	LYS37
B	PHE38
B	PRO39
B	ARG41
B	PHE69
B	ARG73
B	ARG94
B	GLY99
B	TYR102
B	LYS143
B	GLU149
B	TYR151
B	LYS187
B	GLY188
B	ILE189
B	HOH4010
B	HOH4011
B	HOH4014
B	HOH4016
B	HOH4017
B	HOH4018
B	HOH4055
B	HOH4538
B	HOH4578
B	HOH4579
B	HOH4725
B	HOH4935

site_id	AC3
Number of Residues	28
Details	BINDING SITE FOR RESIDUE T5A C 217

Chain	Residue
C	ASP14
C	ARG15
C	THR16
C	GLY17
C	LYS18
C	THR19
C	THR20
C	LYS37
C	PHE38
C	PRO39
C	ARG41
C	PHE69
C	ARG73
C	ARG94
C	SER98
C	GLY99
C	TYR102
C	TYR151
C	LYS187
C	GLY188
C	ILE189
C	HOH4173
C	HOH4174
C	HOH4177
C	HOH4180
C	HOH4181
C	HOH4561
C	HOH4946

site_id	AC4
Number of Residues	31
Details	BINDING SITE FOR RESIDUE T5A D 217

Chain	Residue
D	ARG15
D	THR16
D	GLY17
D	LYS18
D	THR19
D	THR20
D	LYS37
D	PHE38
D	ARG41
D	PHE69
D	ARG73
D	ARG94
D	GLY99
D	TYR102
D	LYS143
D	GLU149
D	TYR151
D	LYS187
D	GLY188
D	ILE189
D	HOH4122
D	HOH4123
D	HOH4126
D	HOH4127
D	HOH4128
D	HOH4129
D	HOH4167
D	HOH4191
D	HOH4221
D	HOH5317
D	ASP14

site_id	AC5
Number of Residues	34
Details	BINDING SITE FOR RESIDUE T5A E 217

Chain	Residue
E	ASP14
E	ARG15
E	THR16
E	GLY17
E	LYS18
E	THR19
E	THR20
E	LYS37
E	PHE38
E	PRO39
E	ARG41
E	LEU53
E	PHE69
E	ARG73
E	ARG94
E	GLY99
E	TYR102
E	GLU142
E	SER144
E	GLU149
E	TYR151
E	LYS187
E	GLY188
E	ILE189
E	HOH4287
E	HOH4288
E	HOH4291
E	HOH4296
E	HOH4297
E	HOH4307
E	HOH4938
E	HOH5329
E	HOH5347
E	HOH5354

site_id	AC6
Number of Residues	34
Details	BINDING SITE FOR RESIDUE T5A F 217

Chain	Residue
F	ASP14
F	ARG15
F	THR16
F	GLY17
F	LYS18
F	THR19
F	THR20
F	LYS37
F	PHE38
F	PRO39
F	ARG41
F	LEU53
F	PHE69
F	ARG73
F	ARG94
F	GLY99
F	TYR102
F	LYS143
F	GLU149
F	TYR151
F	LYS187
F	GLY188
F	ILE189
F	HOH4237
F	HOH4238
F	HOH4241
F	HOH4242
F	HOH4244
F	HOH4281
F	HOH4836
F	HOH4841
F	HOH5082
F	HOH5127
F	HOH5136

site_id	AC7
Number of Residues	36
Details	BINDING SITE FOR RESIDUE T5A G 217

Chain	Residue
G	ASP14
G	ARG15
G	THR16
G	GLY17
G	LYS18
G	THR19
G	THR20
G	LYS37
G	PHE38
G	PRO39
G	ARG41
G	LEU53
G	PHE69
G	ARG73
G	ARG94
G	GLY99
G	TYR102
G	GLU142
G	LYS143
G	SER144
G	GLU149
G	TYR151
G	LYS187
G	GLY188
G	ILE189
G	HOH4404
G	HOH4405
G	HOH4409
G	HOH4412
G	HOH4413
G	HOH4414
G	HOH4532
G	HOH4535
G	HOH4585
G	HOH4643
G	HOH4928

site_id	AC8
Number of Residues	34
Details	BINDING SITE FOR RESIDUE T5A H 217

Chain	Residue
H	ASP14
H	ARG15
H	THR16
H	GLY17
H	LYS18
H	THR19
H	THR20
H	LYS37
H	PHE38
H	PRO39
H	ARG41
H	LEU53
H	PHE69
H	ARG73
H	ARG94
H	GLY99
H	TYR102
H	GLU149
H	TYR151
H	LYS187
H	GLY188
H	ILE189
H	HOH4347
H	HOH4348
H	HOH4351
H	HOH4353
H	HOH4354
H	HOH4355
H	HOH4397
H	HOH4503
H	HOH4608
H	HOH4803
H	HOH4808
H	HOH5010

Functional Information from PROSITE/UniProt

site_id	PS01331
Number of Residues	13
Details	THYMIDYLATE_KINASE Thymidylate kinase signature. VMDRYvySGvAYS

Chain	Residue	Details
A	VAL91-SER103

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	BINDING: BINDING => ECO:0000305

Chain	Residue	Details
A	GLY12
B	GLY12
C	GLY12
D	GLY12
E	GLY12
F	GLY12
G	GLY12
H	GLY12

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