Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3GWC

Crystal structure of Mycobacterium tuberculosis thymidylate synthase X bound to FdUMP and FAD

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004799	molecular_function	thymidylate synthase activity
A	0006231	biological_process	dTMP biosynthetic process
A	0006235	biological_process	dTTP biosynthetic process
A	0008168	molecular_function	methyltransferase activity
A	0009165	biological_process	nucleotide biosynthetic process
A	0016740	molecular_function	transferase activity
A	0032259	biological_process	methylation
A	0050660	molecular_function	flavin adenine dinucleotide binding
A	0050797	molecular_function	thymidylate synthase (FAD) activity
A	0070402	molecular_function	NADPH binding
B	0004799	molecular_function	thymidylate synthase activity
B	0006231	biological_process	dTMP biosynthetic process
B	0006235	biological_process	dTTP biosynthetic process
B	0008168	molecular_function	methyltransferase activity
B	0009165	biological_process	nucleotide biosynthetic process
B	0016740	molecular_function	transferase activity
B	0032259	biological_process	methylation
B	0050660	molecular_function	flavin adenine dinucleotide binding
B	0050797	molecular_function	thymidylate synthase (FAD) activity
B	0070402	molecular_function	NADPH binding
C	0004799	molecular_function	thymidylate synthase activity
C	0006231	biological_process	dTMP biosynthetic process
C	0006235	biological_process	dTTP biosynthetic process
C	0008168	molecular_function	methyltransferase activity
C	0009165	biological_process	nucleotide biosynthetic process
C	0016740	molecular_function	transferase activity
C	0032259	biological_process	methylation
C	0050660	molecular_function	flavin adenine dinucleotide binding
C	0050797	molecular_function	thymidylate synthase (FAD) activity
C	0070402	molecular_function	NADPH binding
D	0004799	molecular_function	thymidylate synthase activity
D	0006231	biological_process	dTMP biosynthetic process
D	0006235	biological_process	dTTP biosynthetic process
D	0008168	molecular_function	methyltransferase activity
D	0009165	biological_process	nucleotide biosynthetic process
D	0016740	molecular_function	transferase activity
D	0032259	biological_process	methylation
D	0050660	molecular_function	flavin adenine dinucleotide binding
D	0050797	molecular_function	thymidylate synthase (FAD) activity
D	0070402	molecular_function	NADPH binding
E	0004799	molecular_function	thymidylate synthase activity
E	0006231	biological_process	dTMP biosynthetic process
E	0006235	biological_process	dTTP biosynthetic process
E	0008168	molecular_function	methyltransferase activity
E	0009165	biological_process	nucleotide biosynthetic process
E	0016740	molecular_function	transferase activity
E	0032259	biological_process	methylation
E	0050660	molecular_function	flavin adenine dinucleotide binding
E	0050797	molecular_function	thymidylate synthase (FAD) activity
E	0070402	molecular_function	NADPH binding
F	0004799	molecular_function	thymidylate synthase activity
F	0006231	biological_process	dTMP biosynthetic process
F	0006235	biological_process	dTTP biosynthetic process
F	0008168	molecular_function	methyltransferase activity
F	0009165	biological_process	nucleotide biosynthetic process
F	0016740	molecular_function	transferase activity
F	0032259	biological_process	methylation
F	0050660	molecular_function	flavin adenine dinucleotide binding
F	0050797	molecular_function	thymidylate synthase (FAD) activity
F	0070402	molecular_function	NADPH binding
G	0004799	molecular_function	thymidylate synthase activity
G	0006231	biological_process	dTMP biosynthetic process
G	0006235	biological_process	dTTP biosynthetic process
G	0008168	molecular_function	methyltransferase activity
G	0009165	biological_process	nucleotide biosynthetic process
G	0016740	molecular_function	transferase activity
G	0032259	biological_process	methylation
G	0050660	molecular_function	flavin adenine dinucleotide binding
G	0050797	molecular_function	thymidylate synthase (FAD) activity
G	0070402	molecular_function	NADPH binding
H	0004799	molecular_function	thymidylate synthase activity
H	0006231	biological_process	dTMP biosynthetic process
H	0006235	biological_process	dTTP biosynthetic process
H	0008168	molecular_function	methyltransferase activity
H	0009165	biological_process	nucleotide biosynthetic process
H	0016740	molecular_function	transferase activity
H	0032259	biological_process	methylation
H	0050660	molecular_function	flavin adenine dinucleotide binding
H	0050797	molecular_function	thymidylate synthase (FAD) activity
H	0070402	molecular_function	NADPH binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	24
Details	BINDING SITE FOR RESIDUE FAD A 259

Chain	Residue
A	ARG95
A	HOH582
A	HOH666
A	HOH862
B	CYS43
B	SER71
B	GLU74
B	HIS98
B	ASN188
B	ARG190
B	FAD259
A	HIS96
D	SER102
D	GLN103
D	SER105
D	UFP260
D	HOH749
A	ARG97
A	HIS98
A	HIS194
A	ARG199
A	HIS203
A	HOH299
A	HOH401

site_id	AC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UFP A 260

Chain	Residue
A	ARG87
A	GLN103
A	LEU104
A	SER105
A	GLN106
A	ARG107
A	ARG172
A	HOH268
A	HOH270
A	HOH566
D	HIS91
D	GLU92
D	ARG95
D	ARG199
D	FAD259

site_id	AC3
Number of Residues	20
Details	BINDING SITE FOR RESIDUE FAD B 259

Chain	Residue
A	CYS43
A	SER71
A	GLU74
A	HIS98
A	ASN188
A	ARG190
A	FAD259
B	ARG95
B	HIS96
B	ARG97
B	HIS98
B	HIS194
B	ARG199
B	HIS203
B	HOH297
B	HOH425
C	SER102
C	GLN103
C	SER105
C	UFP260

site_id	AC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UFP B 260

Chain	Residue
B	ARG87
B	GLN103
B	LEU104
B	SER105
B	GLN106
B	ARG107
B	TYR108
B	ARG172
B	HOH301
B	HOH313
C	HIS91
C	GLU92
C	ARG95
C	ARG199
C	FAD259

site_id	AC5
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FAD C 259

Chain	Residue
B	SER102
B	GLN103
B	SER105
B	UFP260
B	HOH755
C	ARG95
C	HIS96
C	ARG97
C	HIS98
C	HIS194
C	ARG199
C	HIS203
C	HOH281
C	HOH404
C	HOH640
C	HOH858
D	CYS43
D	SER71
D	GLU74
D	HIS98
D	ASN188
D	ARG190
D	FAD259

site_id	AC6
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UFP C 260

Chain	Residue
B	ARG95
B	ARG199
B	FAD259
C	ARG87
C	GLN103
C	LEU104
C	SER105
C	GLN106
C	ARG107
C	TYR108
C	ARG172
C	HOH263
C	HOH268
B	HIS91
B	GLU92

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL C 261

Chain	Residue
C	ARG41
C	SER46
C	ASN51
C	THR54
C	TYR60
C	HIS63

site_id	AC8
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FAD D 259

Chain	Residue
A	SER102
A	GLN103
A	SER105
A	UFP260
C	CYS43
C	SER71
C	GLU74
C	HIS98
C	ASN188
C	ARG190
C	FAD259
D	ARG95
D	HIS96
D	ARG97
D	HIS98
D	HIS194
D	MET198
D	ARG199
D	HIS203
D	HOH263
D	HOH295
D	HOH369
D	HOH633

site_id	AC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UFP D 260

Chain	Residue
A	HIS91
A	GLU92
A	ARG95
A	ARG199
A	FAD259
D	ARG87
D	GLN103
D	LEU104
D	SER105
D	GLN106
D	ARG107
D	TYR108
D	ARG172
D	HOH261
D	HOH267

site_id	BC1
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FAD E 259

Chain	Residue
E	ARG95
E	HIS96
E	ARG97
E	HIS98
E	HIS194
E	ARG199
E	HIS203
E	HOH288
E	HOH345
E	HOH584
E	HOH924
F	CYS43
F	SER71
F	GLU74
F	HIS98
F	ASN188
F	ARG190
F	FAD259
H	SER102
H	GLN103
H	SER105
H	UFP260
H	HOH648

site_id	BC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UFP E 260

Chain	Residue
E	ARG87
E	GLN103
E	LEU104
E	SER105
E	GLN106
E	ARG107
E	TYR108
E	ARG172
E	HOH265
H	HIS91
H	GLU92
H	ARG95
H	ARG199
H	FAD259
H	HOH284

site_id	BC3
Number of Residues	22
Details	BINDING SITE FOR RESIDUE FAD F 259

Chain	Residue
E	CYS43
E	SER71
E	GLU74
E	HIS98
E	ASN188
E	ARG190
E	FAD259
F	ARG95
F	HIS96
F	ARG97
F	HIS98
F	HIS194
F	ARG199
F	HIS203
F	HOH268
F	HOH551
F	HOH930
G	SER102
G	GLN103
G	SER105
G	TYR108
G	UFP260

site_id	BC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UFP F 260

Chain	Residue
F	ARG87
F	GLN103
F	LEU104
F	SER105
F	GLN106
F	ARG107
F	TYR108
F	ARG172
F	HOH265
F	HOH836
G	HIS91
G	GLU92
G	ARG95
G	ARG199
G	FAD259

site_id	BC5
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FAD G 259

Chain	Residue
F	SER102
F	GLN103
F	SER105
F	UFP260
F	HOH853
G	ARG95
G	HIS96
G	ARG97
G	HIS98
G	HIS194
G	ARG199
G	HIS203
G	HOH273
G	HOH641
G	HOH656
G	HOH928
H	CYS43
H	SER71
H	GLU74
H	HIS98
H	ASN188
H	ARG190
H	FAD259

site_id	BC6
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UFP G 260

Chain	Residue
F	HIS91
F	GLU92
F	ARG95
F	ARG199
F	FAD259
F	HOH358
G	ARG87
G	GLN103
G	LEU104
G	SER105
G	GLN106
G	ARG107
G	TYR108
G	ARG172
G	HOH264

site_id	BC7
Number of Residues	24
Details	BINDING SITE FOR RESIDUE FAD H 259

Chain	Residue
E	SER102
E	GLN103
E	SER105
E	TYR108
E	UFP260
E	HOH486
G	CYS43
G	SER71
G	GLU74
G	HIS98
G	ASN188
G	ARG190
G	FAD259
H	ARG95
H	HIS96
H	ARG97
H	HIS98
H	HIS194
H	MET198
H	ARG199
H	HIS203
H	HOH398
H	HOH518
H	HOH718

site_id	BC8
Number of Residues	15
Details	BINDING SITE FOR RESIDUE UFP H 260

Chain	Residue
E	HIS91
E	GLU92
E	ARG95
E	ARG199
E	FAD259
E	HOH261
H	ARG87
H	GLN103
H	LEU104
H	SER105
H	GLN106
H	ARG107
H	TYR108
H	ARG172
H	HOH293

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1582
Details	Domain: {"description":"ThyX","evidences":[{"source":"PROSITE-ProRule","id":"PRU00661","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	80
Details	Motif: {"description":"ThyX motif","evidences":[{"source":"HAMAP-Rule","id":"MF_01408","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Active site: {"description":"Involved in ionization of N3 of dUMP, leading to its activation","evidences":[{"source":"HAMAP-Rule","id":"MF_01408","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	56
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16139296","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2AF6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3GWC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3HZG","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	48
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"16139296","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2AF6","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	32
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16139296","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2AF6","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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