Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4ISK

Crystal structure of E.coli thymidylate synthase with dUMP and the BGC 945 inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003723	molecular_function	RNA binding
A	0004799	molecular_function	thymidylate synthase activity
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006231	biological_process	dTMP biosynthetic process
A	0006235	biological_process	dTTP biosynthetic process
A	0006417	biological_process	regulation of translation
A	0008168	molecular_function	methyltransferase activity
A	0009165	biological_process	nucleotide biosynthetic process
A	0009314	biological_process	response to radiation
A	0016740	molecular_function	transferase activity
A	0016741	molecular_function	transferase activity, transferring one-carbon groups
A	0032259	biological_process	methylation
A	0042803	molecular_function	protein homodimerization activity
B	0000287	molecular_function	magnesium ion binding
B	0003723	molecular_function	RNA binding
B	0004799	molecular_function	thymidylate synthase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006231	biological_process	dTMP biosynthetic process
B	0006235	biological_process	dTTP biosynthetic process
B	0006417	biological_process	regulation of translation
B	0008168	molecular_function	methyltransferase activity
B	0009165	biological_process	nucleotide biosynthetic process
B	0009314	biological_process	response to radiation
B	0016740	molecular_function	transferase activity
B	0016741	molecular_function	transferase activity, transferring one-carbon groups
B	0032259	biological_process	methylation
B	0042803	molecular_function	protein homodimerization activity
C	0000287	molecular_function	magnesium ion binding
C	0003723	molecular_function	RNA binding
C	0004799	molecular_function	thymidylate synthase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006231	biological_process	dTMP biosynthetic process
C	0006235	biological_process	dTTP biosynthetic process
C	0006417	biological_process	regulation of translation
C	0008168	molecular_function	methyltransferase activity
C	0009165	biological_process	nucleotide biosynthetic process
C	0009314	biological_process	response to radiation
C	0016740	molecular_function	transferase activity
C	0016741	molecular_function	transferase activity, transferring one-carbon groups
C	0032259	biological_process	methylation
C	0042803	molecular_function	protein homodimerization activity
D	0000287	molecular_function	magnesium ion binding
D	0003723	molecular_function	RNA binding
D	0004799	molecular_function	thymidylate synthase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006231	biological_process	dTMP biosynthetic process
D	0006235	biological_process	dTTP biosynthetic process
D	0006417	biological_process	regulation of translation
D	0008168	molecular_function	methyltransferase activity
D	0009165	biological_process	nucleotide biosynthetic process
D	0009314	biological_process	response to radiation
D	0016740	molecular_function	transferase activity
D	0016741	molecular_function	transferase activity, transferring one-carbon groups
D	0032259	biological_process	methylation
D	0042803	molecular_function	protein homodimerization activity
E	0000287	molecular_function	magnesium ion binding
E	0003723	molecular_function	RNA binding
E	0004799	molecular_function	thymidylate synthase activity
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006231	biological_process	dTMP biosynthetic process
E	0006235	biological_process	dTTP biosynthetic process
E	0006417	biological_process	regulation of translation
E	0008168	molecular_function	methyltransferase activity
E	0009165	biological_process	nucleotide biosynthetic process
E	0009314	biological_process	response to radiation
E	0016740	molecular_function	transferase activity
E	0016741	molecular_function	transferase activity, transferring one-carbon groups
E	0032259	biological_process	methylation
E	0042803	molecular_function	protein homodimerization activity
F	0000287	molecular_function	magnesium ion binding
F	0003723	molecular_function	RNA binding
F	0004799	molecular_function	thymidylate synthase activity
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006231	biological_process	dTMP biosynthetic process
F	0006235	biological_process	dTTP biosynthetic process
F	0006417	biological_process	regulation of translation
F	0008168	molecular_function	methyltransferase activity
F	0009165	biological_process	nucleotide biosynthetic process
F	0009314	biological_process	response to radiation
F	0016740	molecular_function	transferase activity
F	0016741	molecular_function	transferase activity, transferring one-carbon groups
F	0032259	biological_process	methylation
F	0042803	molecular_function	protein homodimerization activity
G	0000287	molecular_function	magnesium ion binding
G	0003723	molecular_function	RNA binding
G	0004799	molecular_function	thymidylate synthase activity
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006231	biological_process	dTMP biosynthetic process
G	0006235	biological_process	dTTP biosynthetic process
G	0006417	biological_process	regulation of translation
G	0008168	molecular_function	methyltransferase activity
G	0009165	biological_process	nucleotide biosynthetic process
G	0009314	biological_process	response to radiation
G	0016740	molecular_function	transferase activity
G	0016741	molecular_function	transferase activity, transferring one-carbon groups
G	0032259	biological_process	methylation
G	0042803	molecular_function	protein homodimerization activity
H	0000287	molecular_function	magnesium ion binding
H	0003723	molecular_function	RNA binding
H	0004799	molecular_function	thymidylate synthase activity
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006231	biological_process	dTMP biosynthetic process
H	0006235	biological_process	dTTP biosynthetic process
H	0006417	biological_process	regulation of translation
H	0008168	molecular_function	methyltransferase activity
H	0009165	biological_process	nucleotide biosynthetic process
H	0009314	biological_process	response to radiation
H	0016740	molecular_function	transferase activity
H	0016741	molecular_function	transferase activity, transferring one-carbon groups
H	0032259	biological_process	methylation
H	0042803	molecular_function	protein homodimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE UMP A 301

Chain	Residue
A	ARG21
A	ASN177
A	HIS207
A	TYR209
A	1JY303
A	HOH405
A	HOH418
A	HOH470
E	ARG126
A	CYS146
A	HIS147
A	GLN165
A	ARG166
A	SER167
A	CYS168
A	ASP169
A	GLY173

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 302

Chain	Residue
A	HOH579
A	HOH580
A	HOH581
A	HOH582
A	HOH583
A	HOH584

site_id	AC3
Number of Residues	27
Details	BINDING SITE FOR RESIDUE 1JY A 303

Chain	Residue
A	HIS51
A	GLU58
A	ILE79
A	TRP80
A	TRP83
A	ASP169
A	LEU172
A	GLY173
A	PHE176
A	ASN177
A	TYR209
A	VAL262
A	ALA263
A	UMP301
A	HOH423
A	HOH432
A	HOH442
A	HOH463
A	HOH473
A	HOH476
A	HOH477
A	HOH505
A	HOH550
A	HOH579
A	HOH580
A	HOH582
C	HOH459

site_id	AC4
Number of Residues	17
Details	BINDING SITE FOR RESIDUE UMC B 301

Chain	Residue
B	ARG21
B	CYS146
B	HIS147
B	GLN165
B	ARG166
B	SER167
B	CYS168
B	ASP169
B	ASN177
B	HIS207
B	TYR209
B	1JY303
B	HOH415
B	HOH499
B	HOH527
B	HOH528
D	ARG126

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 302

Chain	Residue
B	HOH564
B	HOH565
B	HOH566
B	HOH567
B	HOH568
B	HOH569

site_id	AC6
Number of Residues	25
Details	BINDING SITE FOR RESIDUE 1JY B 303

Chain	Residue
B	HIS51
B	GLU58
B	ILE79
B	TRP80
B	TRP83
B	LEU143
B	ASP169
B	LEU172
B	GLY173
B	PHE176
B	ASN177
B	TYR209
B	VAL262
B	ALA263
B	UMC301
B	HOH425
B	HOH431
B	HOH436
B	HOH437
B	HOH449
B	HOH469
B	HOH523
B	HOH565
B	HOH566
B	HOH569

site_id	AC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UMP C 301

Chain	Residue
C	CYS146
C	HIS147
C	GLN165
C	ARG166
C	SER167
C	CYS168
C	ASP169
C	ASN177
C	HIS207
C	TYR209
C	1JY303
C	HOH414
F	ARG126
F	ARG127
C	ARG21

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 302

Chain	Residue
C	HOH563
C	HOH564
C	HOH565
C	HOH566
C	HOH567
C	HOH568

site_id	AC9
Number of Residues	26
Details	BINDING SITE FOR RESIDUE 1JY C 303

Chain	Residue
A	PRO256
C	HIS51
C	ILE79
C	TRP80
C	TRP83
C	LEU143
C	ASP169
C	LEU172
C	GLY173
C	PHE176
C	ASN177
C	TYR209
C	VAL262
C	ALA263
C	UMP301
C	HOH404
C	HOH406
C	HOH410
C	HOH413
C	HOH432
C	HOH445
C	HOH518
C	HOH564
C	HOH566
C	HOH567
C	HOH568

site_id	BC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE UMC D 301

Chain	Residue
B	ARG126
B	ARG127
D	ARG21
D	CYS146
D	HIS147
D	GLN165
D	ARG166
D	SER167
D	CYS168
D	ASP169
D	GLY173
D	ASN177
D	HIS207
D	TYR209
D	1JY303
D	HOH436

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 302

Chain	Residue
D	HOH526
D	HOH527
D	HOH528
D	HOH529
D	HOH530
D	HOH531

site_id	BC3
Number of Residues	28
Details	BINDING SITE FOR RESIDUE 1JY D 303

Chain	Residue
D	HIS51
D	GLU58
D	ILE79
D	TRP80
D	TRP83
D	ASP169
D	LEU172
D	GLY173
D	PHE176
D	ASN177
D	TYR209
D	VAL262
D	ALA263
D	UMC301
D	HOH406
D	HOH413
D	HOH429
D	HOH437
D	HOH441
D	HOH442
D	HOH492
D	HOH499
D	HOH525
D	HOH526
D	HOH528
D	HOH529
E	HOH440
E	HOH488

site_id	BC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UMC E 301

Chain	Residue
A	ARG126
E	ARG21
E	CYS146
E	HIS147
E	GLN165
E	ARG166
E	SER167
E	CYS168
E	ASP169
E	ASN177
E	HIS207
E	TYR209
E	1JY303
E	HOH409
E	HOH436

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 302

Chain	Residue
E	THR78
E	HOH525
E	HOH526
E	HOH527
E	HOH528
E	HOH529

site_id	BC6
Number of Residues	24
Details	BINDING SITE FOR RESIDUE 1JY E 303

Chain	Residue
D	PRO256
E	HIS51
E	SER54
E	GLU58
E	THR78
E	ILE79
E	TRP80
E	TRP83
E	ASP169
E	LEU172
E	GLY173
E	PHE176
E	ASN177
E	TYR209
E	VAL262
E	ALA263
E	UMC301
E	HOH421
E	HOH426
E	HOH458
E	HOH484
E	HOH511
E	HOH527
E	HOH528

site_id	BC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE UMC F 301

Chain	Residue
C	ARG126
F	ARG21
F	CYS146
F	HIS147
F	GLN165
F	ARG166
F	SER167
F	CYS168
F	ASP169
F	ASN177
F	HIS207
F	TYR209
F	1JY302
F	HOH423

site_id	BC8
Number of Residues	15
Details	BINDING SITE FOR RESIDUE 1JY F 302

Chain	Residue
F	HIS51
F	ILE79
F	TRP83
F	ASP169
F	LEU172
F	GLY173
F	PHE176
F	ASN177
F	TYR209
F	VAL262
F	ALA263
F	UMC301
H	PRO256
H	GLY257
H	ILE258

site_id	BC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UMP G 301

Chain	Residue
G	ARG21
G	CYS146
G	HIS147
G	GLN165
G	ARG166
G	SER167
G	CYS168
G	ASP169
G	GLY173
G	ASN177
G	HIS207
G	TYR209
G	1JY303
G	HOH425
H	ARG126

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG G 302

Chain	Residue
G	HOH469
G	HOH470
G	HOH471
G	HOH472
G	HOH473
G	HOH474

site_id	CC2
Number of Residues	25
Details	BINDING SITE FOR RESIDUE 1JY G 303

Chain	Residue
B	PRO256
G	HIS51
G	GLU58
G	THR78
G	ILE79
G	TRP80
G	TRP83
G	ASP169
G	LEU172
G	GLY173
G	PHE176
G	ASN177
G	TYR209
G	VAL262
G	ALA263
G	UMP301
G	HOH409
G	HOH413
G	HOH418
G	HOH422
G	HOH430
G	HOH435
G	HOH471
G	HOH473
G	HOH474

site_id	CC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE UMC H 301

Chain	Residue
G	ARG126
H	ARG21
H	CYS146
H	HIS147
H	GLN165
H	ARG166
H	SER167
H	CYS168
H	ASP169
H	ASN177
H	HIS207
H	TYR209
H	1JY303
H	HOH432

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG H 302

Chain	Residue
H	HOH448
H	HOH449
H	HOH450
H	HOH451
H	HOH452
H	HOH453

site_id	CC5
Number of Residues	20
Details	BINDING SITE FOR RESIDUE 1JY H 303

Chain	Residue
F	LYS259
H	GLU58
H	ILE79
H	TRP80
H	TRP83
H	ASP169
H	LEU172
H	GLY173
H	PHE176
H	ASN177
H	TYR209
H	VAL262
H	ALA263
H	UMC301
H	HOH414
H	HOH416
H	HOH420
H	HOH450
H	HOH452
H	HOH453

Functional Information from PROSITE/UniProt

site_id	PS00091
Number of Residues	29
Details	THYMIDYLATE_SYNTHASE Thymidylate synthase active site. RriIvsaWNvgeldkma.....LaPCHaffQFyV

Chain	Residue	Details
A	ARG126-VAL154

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"HAMAP-Rule","id":"MF_00008","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"2223754","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8973201","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9416600","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	56
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"2223754","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8973201","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1KCE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2TSC","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8312270","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1TYS","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"2223754","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8973201","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1KCE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2TSC","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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