Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3AH5

Crystal Structure of flavin dependent thymidylate synthase ThyX from helicobacter pylori complexed with FAD and dUMP

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE UMP A 241

Chain	Residue
A	ARG89
C	ARG97
C	ARG197
C	FAD240
C	HOH243
C	HOH244
A	LEU92
A	SER107
A	SER108
A	ARG109
A	LYS170
C	HOH3
C	GLN93
C	GLU94

site_id	AC2
Number of Residues	27
Details	BINDING SITE FOR RESIDUE FAD A 240

Chain	Residue
A	ARG97
A	HIS98
A	ARG99
A	ILE100
A	ASN192
A	LEU196
A	ARG197
A	LYS201
A	HOH245
A	HOH249
A	HOH252
A	HOH264
A	HOH338
B	CYS44
B	ARG70
B	SER73
B	GLU76
B	ILE100
B	ASN186
B	ARG188
B	FAD240
C	SER104
C	VAL105
C	SER107
C	TYR110
C	UMP241
C	HOH245

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 5

Chain	Residue
A	PRO218
A	GLY219
A	HOH317

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 A 10

Chain	Residue
A	HIS234
A	HIS236
A	HIS237
A	HOH325
A	HOH448
B	PHE69
B	ARG70
C	HOH449

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 11

Chain	Residue
A	ASN67
A	ILE68
A	PHE69
A	HOH287
D	LYS201

site_id	AC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE UMP B 241

Chain	Residue
B	HOH4
B	ARG89
B	SER107
B	SER108
B	ARG109
B	LYS170
D	HOH13
D	GLN93
D	GLU94
D	ARG97
D	ARG197
D	FAD240
D	HOH266

site_id	AC7
Number of Residues	30
Details	BINDING SITE FOR RESIDUE FAD B 240

Chain	Residue
D	HOH275
A	CYS44
A	ARG70
A	HIS71
A	SER73
A	GLU76
A	ILE100
A	ASN186
A	ARG188
A	FAD240
B	HOH11
B	ARG97
B	HIS98
B	ARG99
B	ILE100
B	ASN192
B	LEU196
B	ARG197
B	LYS201
B	HOH247
B	HOH254
B	HOH266
B	HOH273
B	HOH341
D	SER104
D	VAL105
D	SER107
D	TYR110
D	UMP241
D	HOH252

site_id	AC8
Number of Residues	28
Details	BINDING SITE FOR RESIDUE FAD C 240

Chain	Residue
A	SER102
A	SER104
A	VAL105
A	SER107
A	TYR110
A	UMP241
A	HOH253
C	HOH1
C	ARG97
C	HIS98
C	ARG99
C	ILE100
C	ASN192
C	LEU196
C	ARG197
C	HOH266
C	HOH288
C	HOH290
C	HOH311
D	CYS44
D	ARG70
D	HIS71
D	SER73
D	GLU76
D	ILE100
D	ASN186
D	ARG188
D	FAD240

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE UMP C 241

Chain	Residue
A	HOH7
A	GLN93
A	GLU94
A	ARG97
A	ARG197
A	FAD240
C	HOH17
C	ARG89
C	LEU92
C	SER107
C	SER108
C	ARG109
C	LYS170

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 4

Chain	Residue
C	PRO218
C	GLY219
C	HOH396
C	HOH406

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 8

Chain	Residue
B	HOH516
C	PRO33
C	LEU34
C	GLU220
C	HIS221

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 C 9

Chain	Residue
C	SER199
C	ASN200

site_id	BC4
Number of Residues	27
Details	BINDING SITE FOR RESIDUE FAD D 240

Chain	Residue
B	SER102
B	SER104
B	VAL105
B	SER107
B	TYR110
B	UMP241
B	HOH246
C	CYS44
C	ARG70
C	HIS71
C	SER73
C	GLU76
C	ILE100
C	ASN186
C	ARG188
C	FAD240
D	HOH15
D	HOH20
D	ARG97
D	HIS98
D	ARG99
D	ILE100
D	ASN192
D	LEU196
D	ARG197
D	HOH245
D	HOH332

site_id	BC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE UMP D 241

Chain	Residue
B	HOH2
B	HOH14
B	GLN93
B	GLU94
B	ARG97
B	ARG197
B	FAD240
B	HOH270
D	ARG89
D	LEU92
D	SER107
D	SER108
D	ARG109

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 3

Chain	Residue
D	PRO123
D	LEU124
E	SO42

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 6

Chain	Residue
D	PRO218
D	GLY219
E	LYS57

site_id	BC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE UMP E 241

Chain	Residue
E	HOH10
E	GLU94
E	ARG97
E	ARG197
E	FAD240
E	HOH257
F	ARG89
F	LEU92
F	SER107
F	SER108
F	ARG109
F	HOH242

site_id	BC9
Number of Residues	24
Details	BINDING SITE FOR RESIDUE FAD E 240

Chain	Residue
E	CYS44
E	ARG70
E	HIS71
E	SER73
E	GLU76
E	ARG97
E	HIS98
E	ARG99
E	ILE100
E	ILE100
E	ASN186
E	ARG188
E	ASN192
E	LEU196
E	ARG197
E	UMP241
E	HOH252
E	HOH254
E	HOH383
F	LEU103
F	SER104
F	VAL105
F	SER107
F	TYR110

site_id	CC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 E 1

Chain	Residue
E	PRO218
E	GLY219

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 2

Chain	Residue
D	SO43
D	LEU122
D	PRO123
D	LEU124
E	LEU122
E	PRO123
E	LEU124

site_id	CC3
Number of Residues	27
Details	BINDING SITE FOR RESIDUE FAD F 240

Chain	Residue
E	SER104
E	VAL105
E	SER107
E	TYR110
E	HOH251
F	CYS44
F	ARG70
F	HIS71
F	SER73
F	GLU76
F	ARG97
F	HIS98
F	ARG99
F	ILE100
F	ILE100
F	ASN186
F	ARG188
F	ASN192
F	LEU196
F	ARG197
F	LYS201
F	UMP241
F	HOH244
F	HOH249
F	HOH258
F	HOH268
F	HOH484

site_id	CC4
Number of Residues	14
Details	BINDING SITE FOR RESIDUE UMP F 241

Chain	Residue
E	HOH18
E	ARG89
E	LEU92
E	SER107
E	SER108
E	ARG109
F	HOH16
F	GLN93
F	GLU94
F	ARG97
F	ARG197
F	FAD240
F	HOH257
F	HOH484

site_id	CC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 F 7

Chain	Residue
F	PRO218
F	GLY219

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	207
Details	Domain: {"description":"ThyX","evidences":[{"source":"PROSITE-ProRule","id":"PRU00661","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	60
Details	Motif: {"description":"ThyX motif","evidences":[{"source":"PubMed","id":"12029065","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
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	60
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22512654","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3AH5","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"22512654","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3AH5","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	6
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"22512654","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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