Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4EB4

Crystal structure of mouse thymidylate synthase in ternary complex with dUMP and Tomudex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000900	molecular_function	mRNA regulatory element binding translation repressor activity
A	0003729	molecular_function	mRNA binding
A	0004799	molecular_function	thymidylate synthase activity
A	0005542	molecular_function	folic acid binding
A	0005634	cellular_component	nucleus
A	0005657	cellular_component	replication fork
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005743	cellular_component	mitochondrial inner membrane
A	0005759	cellular_component	mitochondrial matrix
A	0005829	cellular_component	cytosol
A	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
A	0006231	biological_process	dTMP biosynthetic process
A	0006235	biological_process	dTTP biosynthetic process
A	0006260	biological_process	DNA replication
A	0006417	biological_process	regulation of translation
A	0008168	molecular_function	methyltransferase activity
A	0009165	biological_process	nucleotide biosynthetic process
A	0016740	molecular_function	transferase activity
A	0016741	molecular_function	transferase activity, transferring one-carbon groups
A	0017148	biological_process	negative regulation of translation
A	0032259	biological_process	methylation
A	0035999	biological_process	tetrahydrofolate interconversion
A	0042803	molecular_function	protein homodimerization activity
A	0046653	biological_process	tetrahydrofolate metabolic process
A	1901363	molecular_function	heterocyclic compound binding
A	1990825	molecular_function	sequence-specific mRNA binding
B	0000900	molecular_function	mRNA regulatory element binding translation repressor activity
B	0003729	molecular_function	mRNA binding
B	0004799	molecular_function	thymidylate synthase activity
B	0005542	molecular_function	folic acid binding
B	0005634	cellular_component	nucleus
B	0005657	cellular_component	replication fork
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005743	cellular_component	mitochondrial inner membrane
B	0005759	cellular_component	mitochondrial matrix
B	0005829	cellular_component	cytosol
B	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
B	0006231	biological_process	dTMP biosynthetic process
B	0006235	biological_process	dTTP biosynthetic process
B	0006260	biological_process	DNA replication
B	0006417	biological_process	regulation of translation
B	0008168	molecular_function	methyltransferase activity
B	0009165	biological_process	nucleotide biosynthetic process
B	0016740	molecular_function	transferase activity
B	0016741	molecular_function	transferase activity, transferring one-carbon groups
B	0017148	biological_process	negative regulation of translation
B	0032259	biological_process	methylation
B	0035999	biological_process	tetrahydrofolate interconversion
B	0042803	molecular_function	protein homodimerization activity
B	0046653	biological_process	tetrahydrofolate metabolic process
B	1901363	molecular_function	heterocyclic compound binding
B	1990825	molecular_function	sequence-specific mRNA binding
C	0000900	molecular_function	mRNA regulatory element binding translation repressor activity
C	0003729	molecular_function	mRNA binding
C	0004799	molecular_function	thymidylate synthase activity
C	0005542	molecular_function	folic acid binding
C	0005634	cellular_component	nucleus
C	0005657	cellular_component	replication fork
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005743	cellular_component	mitochondrial inner membrane
C	0005759	cellular_component	mitochondrial matrix
C	0005829	cellular_component	cytosol
C	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
C	0006231	biological_process	dTMP biosynthetic process
C	0006235	biological_process	dTTP biosynthetic process
C	0006260	biological_process	DNA replication
C	0006417	biological_process	regulation of translation
C	0008168	molecular_function	methyltransferase activity
C	0009165	biological_process	nucleotide biosynthetic process
C	0016740	molecular_function	transferase activity
C	0016741	molecular_function	transferase activity, transferring one-carbon groups
C	0017148	biological_process	negative regulation of translation
C	0032259	biological_process	methylation
C	0035999	biological_process	tetrahydrofolate interconversion
C	0042803	molecular_function	protein homodimerization activity
C	0046653	biological_process	tetrahydrofolate metabolic process
C	1901363	molecular_function	heterocyclic compound binding
C	1990825	molecular_function	sequence-specific mRNA binding
D	0000900	molecular_function	mRNA regulatory element binding translation repressor activity
D	0003729	molecular_function	mRNA binding
D	0004799	molecular_function	thymidylate synthase activity
D	0005542	molecular_function	folic acid binding
D	0005634	cellular_component	nucleus
D	0005657	cellular_component	replication fork
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005743	cellular_component	mitochondrial inner membrane
D	0005759	cellular_component	mitochondrial matrix
D	0005829	cellular_component	cytosol
D	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
D	0006231	biological_process	dTMP biosynthetic process
D	0006235	biological_process	dTTP biosynthetic process
D	0006260	biological_process	DNA replication
D	0006417	biological_process	regulation of translation
D	0008168	molecular_function	methyltransferase activity
D	0009165	biological_process	nucleotide biosynthetic process
D	0016740	molecular_function	transferase activity
D	0016741	molecular_function	transferase activity, transferring one-carbon groups
D	0017148	biological_process	negative regulation of translation
D	0032259	biological_process	methylation
D	0035999	biological_process	tetrahydrofolate interconversion
D	0042803	molecular_function	protein homodimerization activity
D	0046653	biological_process	tetrahydrofolate metabolic process
D	1901363	molecular_function	heterocyclic compound binding
D	1990825	molecular_function	sequence-specific mRNA binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE UMP A 401

Chain	Residue
A	ARG44
A	HIS250
A	TYR252
A	D16402
A	HOH502
A	HOH625
B	ARG169
B	ARG170
A	CYS189
A	HIS190
A	GLN208
A	ARG209
A	SER210
A	GLY211
A	ASP212
A	ASN220

site_id	AC2
Number of Residues	21
Details	BINDING SITE FOR RESIDUE D16 A 402

Chain	Residue
A	PHE74
A	ILE102
A	TRP103
A	ASP212
A	LEU215
A	GLY216
A	PHE219
A	ASN220
A	TYR252
A	LYS302
A	MET303
A	MET305
A	ALA306
A	UMP401
A	HOH517
A	HOH635
A	HOH665
A	HOH684
A	HOH746
A	HOH855
A	HOH893

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DTT A 403

Chain	Residue
A	GLN154
A	LYS157
A	VAL158
A	THR161
A	ASP168
A	ARG170
A	ILE172
A	HOH550
A	HOH562
A	HOH631
A	HOH793
B	LEU181

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 404

Chain	Residue
A	ASP167
A	VAL198
A	ASN199
A	HOH645
A	HOH767
B	LYS40
B	LYS41
B	GLU42

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 405

Chain	Residue
A	ASN177
A	LYS179
A	HOH702
A	HOH853
B	GLY137
B	ASN177
B	LYS179

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL A 406

Chain	Residue
A	HOH618
A	HOH628

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 407

Chain	Residue
A	ARG277
A	LYS278
A	HOH797
B	LYS87
B	LYS98

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 408

Chain	Residue
A	ARG268
A	PRO297
A	HIS298
A	PRO299

site_id	AC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UMP B 401

Chain	Residue
A	ARG169
A	ARG170
B	ARG44
B	CYS189
B	HIS190
B	GLN208
B	ARG209
B	SER210
B	ASP212
B	ASN220
B	HIS250
B	TYR252
B	D16402
B	HOH595
B	HOH838

site_id	BC1
Number of Residues	21
Details	BINDING SITE FOR RESIDUE D16 B 402

Chain	Residue
B	LYS302
B	MET303
B	MET305
B	ALA306
B	UMP401
B	HOH570
B	HOH612
B	HOH679
B	HOH680
B	HOH715
B	HOH774
B	HOH832
B	PHE74
B	ILE102
B	TRP103
B	ASN106
B	ASP212
B	LEU215
B	GLY216
B	PHE219
B	TYR252

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL B 403

Chain	Residue
B	LEU115
B	LEU181
B	PRO182
B	MET184
B	PRO187
B	HOH512
B	HOH532
B	HOH738
B	HOH796
B	HOH846

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL B 404

Chain	Residue
A	LYS40
A	LYS41
A	GLU42
A	HOH741
B	ASP167
B	VAL198
B	ASN199
B	HOH740

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL B 405

Chain	Residue
B	HIS22
B	GLU24
B	LEU25
B	PRO269
B	HOH566

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MES B 406

Chain	Residue
B	ARG36
B	CYS37
B	GLY38
B	PHE39
B	LYS40
B	HOH843

site_id	BC6
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UMP C 401

Chain	Residue
C	ARG44
C	CYS189
C	HIS190
C	ARG209
C	SER210
C	ASP212
C	GLY216
C	ASN220
C	HIS250
C	TYR252
C	D16402
C	HOH505
C	HOH694
D	ARG169
D	ARG170

site_id	BC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE D16 C 402

Chain	Residue
C	PHE74
C	ARG101
C	ASP212
C	LEU215
C	GLY216
C	PHE219
C	TYR252
C	UMP401
C	HOH564
C	HOH618
C	HOH622
C	HOH680
C	HOH741

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL C 403

Chain	Residue
C	ARG21
C	ARG58
C	HOH606
C	HOH754

site_id	BC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UMP D 401

Chain	Residue
C	ARG169
C	ARG170
D	ARG44
D	CYS189
D	HIS190
D	ARG209
D	SER210
D	GLY211
D	ASP212
D	GLY216
D	ASN220
D	HIS250
D	TYR252
D	D16402
D	HOH566

site_id	CC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE D16 D 402

Chain	Residue
D	PHE74
D	ILE102
D	ASP212
D	LEU215
D	GLY216
D	PHE219
D	TYR252
D	LYS302
D	MET303
D	UMP401
D	HOH603
D	HOH686
D	HOH699

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 403

Chain	Residue
D	ARG36
D	CYS37
D	GLY38
D	PHE39
D	GOL404

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL D 404

Chain	Residue
C	ASN199
D	PHE39
D	LYS40
D	GOL403

Functional Information from PROSITE/UniProt

site_id	PS00091
Number of Residues	29
Details	THYMIDYLATE_SYNTHASE Thymidylate synthase active site. RriImcaWNpkdlplma.....LpPCHalcQFyV

Chain	Residue	Details
A	ARG169-VAL197

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"UniProtKB","id":"P0A884","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Binding site: {"description":"in other chain","evidences":[{"source":"UniProtKB","id":"P0A884","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P45352","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	24
Details	Binding site: {"description":"in other chain","evidences":[{"source":"UniProtKB","id":"P45352","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P0A884","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P04818","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"UniProtKB","id":"P04818","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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