Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2AF6

Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)

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	2
Details	BINDING SITE FOR RESIDUE IOD A 3001

Chain	Residue
A	ALA247
A	HOH4737

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE IOD D 3002

Chain	Residue
C	FAD2600
D	PHE70
D	SER71
D	GOL2012

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD G 3003

Chain	Residue
G	THR54
G	HOH6715

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE IOD D 3004

Chain	Residue
D	VAL222
D	HOH3122
D	HOH3123
D	HOH3124
D	TYR189

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE IOD F 3005

Chain	Residue
F	LYS14
F	THR15
F	GLY32
F	TYR189
F	VAL222
F	HOH7704

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD E 3006

Chain	Residue
E	VAL23
G	GLN10

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD E 3007

Chain	Residue
E	THR4

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD A 3008

Chain	Residue
A	THR4

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD C 3009

Chain	Residue
C	THR4

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE IOD F 3010

Chain	Residue
F	ARG41
F	PRO50
F	THR54
F	GOL2014
F	HOH7707

site_id	BC2
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FAD D 1600

Chain	Residue
A	SER102
A	GLN103
A	SER105
C	CYS43
C	SER71
C	GLU74
C	HIS98
C	ASN188
C	ARG190
C	FAD2600
D	ARG95
D	HIS96
D	ARG97
D	HIS98
D	HIS194
D	MSE198
D	ARG199
D	HIS203
D	BRU1603
D	HOH3026
D	HOH3040
D	HOH3050
D	HOH3054

site_id	BC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE BRU D 1603

Chain	Residue
A	ARG87
A	GLN103
A	LEU104
A	SER105
A	GLN106
A	ARG107
A	ARG172
D	HIS91
D	GLU92
D	ARG95
D	ARG199
D	FAD1600
D	HOH3014
D	HOH3019

site_id	BC4
Number of Residues	26
Details	BINDING SITE FOR RESIDUE FAD C 2600

Chain	Residue
B	SER102
B	GLN103
B	SER105
B	HOH3689
C	ARG95
C	HIS96
C	ARG97
C	HIS98
C	HIS194
C	MSE198
C	ARG199
C	HIS203
C	BRU2603
C	HOH3060
C	HOH3074
C	HOH3076
C	HOH3078
D	CYS43
D	SER71
D	GLU74
D	HIS98
D	ASN188
D	ARG190
D	FAD1600
D	GOL2012
D	IOD3002

site_id	BC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE BRU C 2603

Chain	Residue
B	ARG172
C	HIS91
C	GLU92
C	ARG95
C	ARG199
C	FAD2600
C	HOH3015
C	HOH3021
B	ARG87
B	GLN103
B	LEU104
B	SER105
B	GLN106
B	ARG107
B	TYR108

site_id	BC6
Number of Residues	25
Details	BINDING SITE FOR RESIDUE FAD B 3600

Chain	Residue
A	CYS43
A	SER71
A	GLU74
A	HIS98
A	ASN188
A	ARG190
A	GOL2013
A	FAD4600
B	ARG95
B	HIS96
B	ARG97
B	HIS98
B	HIS194
B	MSE198
B	ARG199
B	HIS203
B	BRU3603
B	HOH3647
B	HOH3660
B	HOH3723
C	SER102
C	GLN103
C	SER105
C	TYR108
C	HOH3073

site_id	BC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE BRU B 3603

Chain	Residue
B	HIS91
B	GLU92
B	ARG95
B	ARG199
B	FAD3600
B	HOH3604
B	HOH3615
C	ARG87
C	GLN103
C	LEU104
C	SER105
C	GLN106
C	ARG107
C	TYR108
C	ARG172

site_id	BC8
Number of Residues	25
Details	BINDING SITE FOR RESIDUE FAD A 4600

Chain	Residue
A	ARG95
A	HIS96
A	ARG97
A	HIS98
A	HIS194
A	MSE198
A	ARG199
A	HIS203
A	BRU4603
A	HOH4627
A	HOH4636
A	HOH4647
A	HOH4701
A	HOH4726
A	HOH4731
B	CYS43
B	SER71
B	GLU74
B	HIS98
B	ASN188
B	ARG190
B	FAD3600
D	SER102
D	GLN103
D	TYR108

site_id	BC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE BRU A 4603

Chain	Residue
A	HIS91
A	GLU92
A	ARG95
A	ARG199
A	FAD4600
A	HOH4606
A	HOH4634
D	ARG87
D	GLN103
D	LEU104
D	SER105
D	GLN106
D	ARG107
D	TYR108
D	ARG172

site_id	CC1
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FAD H 5600

Chain	Residue
E	SER102
E	GLN103
E	TYR108
E	HOH8648
E	HOH8676
G	CYS43
G	SER71
G	HIS98
G	ASN188
G	ARG190
G	FAD6600
H	ARG95
H	HIS96
H	ARG97
H	HIS98
H	HIS194
H	MSE198
H	ARG199
H	HIS203
H	BRU5603
H	HOH5664
H	HOH5670
H	HOH5689

site_id	CC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE BRU H 5603

Chain	Residue
E	ARG87
E	GLN103
E	LEU104
E	SER105
E	GLN106
E	ARG107
E	TYR108
E	ARG172
H	HIS91
H	GLU92
H	ARG95
H	ARG199
H	FAD5600
H	HOH5606
H	HOH5614

site_id	CC3
Number of Residues	22
Details	BINDING SITE FOR RESIDUE FAD G 6600

Chain	Residue
F	SER102
F	GLN103
F	SER105
F	HOH7634
F	HOH7690
G	ARG95
G	HIS96
G	ARG97
G	HIS98
G	HIS194
G	MSE198
G	ARG199
G	BRU6603
G	HOH6656
G	HOH6658
H	CYS43
H	SER71
H	GLU74
H	HIS98
H	ASN188
H	ARG190
H	FAD5600

site_id	CC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE BRU G 6603

Chain	Residue
F	ARG87
F	GLN103
F	LEU104
F	SER105
F	GLN106
F	ARG107
F	TYR108
F	ARG172
G	HIS91
G	GLU92
G	ARG95
G	ARG199
G	FAD6600
G	HOH6607
G	HOH6624

site_id	CC5
Number of Residues	25
Details	BINDING SITE FOR RESIDUE FAD F 7600

Chain	Residue
E	CYS43
E	SER71
E	GLU74
E	HIS98
E	ASN188
E	ARG190
E	FAD8600
F	ARG95
F	HIS96
F	ARG97
F	HIS98
F	HIS194
F	MSE198
F	ARG199
F	HIS203
F	BRU7603
F	HOH7624
F	HOH7653
F	HOH7659
F	HOH7696
G	SER102
G	GLN103
G	SER105
G	TYR108
G	HOH6706

site_id	CC6
Number of Residues	15
Details	BINDING SITE FOR RESIDUE BRU F 7603

Chain	Residue
F	HIS91
F	GLU92
F	ARG95
F	ARG199
F	FAD7600
F	HOH7606
F	HOH7613
G	ARG87
G	GLN103
G	LEU104
G	SER105
G	GLN106
G	ARG107
G	TYR108
G	ARG172

site_id	CC7
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FAD E 8600

Chain	Residue
E	ARG95
E	HIS96
E	ARG97
E	HIS98
E	HIS194
E	MSE198
E	ARG199
E	HIS203
E	BRU8603
E	HOH8661
E	HOH8666
E	HOH8688
F	CYS43
F	SER71
F	GLU74
F	HIS98
F	ASN188
F	ARG190
F	GOL2007
F	FAD7600
H	SER102
H	GLN103
H	SER105

site_id	CC8
Number of Residues	15
Details	BINDING SITE FOR RESIDUE BRU E 8603

Chain	Residue
E	HIS91
E	GLU92
E	ARG95
E	ARG199
E	FAD8600
E	HOH8604
E	HOH8605
H	ARG87
H	GLN103
H	LEU104
H	SER105
H	GLN106
H	ARG107
H	TYR108
H	ARG172

site_id	CC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 2001

Chain	Residue
A	LYS14
A	THR15
A	GLY32
A	SER77
A	VAL78
A	TYR189
A	HOH4702

site_id	DC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL B 2002

Chain	Residue
B	LYS14
B	THR15
B	GLY31
B	GLY32
B	SER77
B	VAL78
B	TYR189
B	VAL222

site_id	DC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 2003

Chain	Residue
C	LYS14
C	THR15
C	GLY31
C	GLY32
C	SER77
C	VAL78
C	TYR189
C	VAL222
C	HOH3093

site_id	DC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL E 2004

Chain	Residue
E	LYS14
E	THR15
E	GLY31
E	GLY32
E	SER77
E	VAL78
E	TYR189
E	VAL222

site_id	DC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL G 2005

Chain	Residue
G	LYS14
G	THR15
G	GLY32
G	SER77
G	VAL78
G	TYR189
G	VAL222
G	HOH6691

site_id	DC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL H 2006

Chain	Residue
H	LYS14
H	THR15
H	GLY31
H	GLY32
H	SER77
H	TYR189
H	VAL222
H	HOH5605

site_id	DC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL F 2007

Chain	Residue
E	FAD8600
F	HIS69
F	SER71
F	HOH7689

site_id	DC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL B 2008

Chain	Residue
B	LEU216
B	ARG217
B	PHE227
B	PHE230
B	HOH3617
B	HOH3645
F	SER48
F	LYS49
F	PRO50

site_id	DC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL D 2009

Chain	Residue
D	ARG41
D	PRO50
D	THR54
D	TYR60

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 2010

Chain	Residue
A	ARG41
A	THR54
A	TYR60

site_id	EC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL E 2011

Chain	Residue
E	ARG87
E	HIS91
E	ASN177
H	ARG87
H	SER88
H	HIS91
H	ASN177

site_id	EC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 2012

Chain	Residue
C	FAD2600
D	HIS69
D	SER71
D	VAL72
D	IOD3002
D	HOH3025
D	HOH3117

site_id	EC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 2013

Chain	Residue
A	HIS69
A	SER71
A	VAL72
A	HOH4619
A	HOH4727
B	FAD3600

site_id	EC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL F 2014

Chain	Residue
F	ARG41
F	PRO50
F	THR54
F	IOD3010
F	HOH7645
F	HOH7706
F	HOH7707

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Involved in ionization of N3 of dUMP, leading to its activation => ECO:0000255\|HAMAP-Rule:MF_01408

Chain	Residue	Details
A	ARG199
B	ARG199
C	ARG199
D	ARG199
E	ARG199
F	ARG199
G	ARG199
H	ARG199

site_id	SWS_FT_FI2
Number of Residues	40
Details	BINDING: BINDING => ECO:0000269\|PubMed:16139296, ECO:0007744\|PDB:2AF6, ECO:0007744\|PDB:3GWC, ECO:0007744\|PDB:3HZG

Chain	Residue	Details
A	SER71
B	HIS194
C	SER71
C	ARG95
C	GLN103
C	ASN188
C	HIS194
D	SER71
D	ARG95
D	GLN103
D	ASN188
A	ARG95
D	HIS194
E	SER71
E	ARG95
E	GLN103
E	ASN188
E	HIS194
F	SER71
F	ARG95
F	GLN103
F	ASN188
A	GLN103
F	HIS194
G	SER71
G	ARG95
G	GLN103
G	ASN188
G	HIS194
H	SER71
H	ARG95
H	GLN103
H	ASN188
A	ASN188
H	HIS194
A	HIS194
B	SER71
B	ARG95
B	GLN103
B	ASN188

site_id	SWS_FT_FI3
Number of Residues	16
Details	BINDING: in other chain => ECO:0000305\|PubMed:16139296, ECO:0007744\|PDB:2AF6

Chain	Residue	Details
A	ARG87
E	ARG172
F	ARG87
F	ARG172
G	ARG87
G	ARG172
H	ARG87
H	ARG172
A	ARG172
B	ARG87
B	ARG172
C	ARG87
C	ARG172
D	ARG87
D	ARG172
E	ARG87

site_id	SWS_FT_FI4
Number of Residues	16
Details	BINDING: BINDING => ECO:0000305\|PubMed:16139296, ECO:0007744\|PDB:2AF6

Chain	Residue	Details
A	GLU92
E	ARG199
F	GLU92
F	ARG199
G	GLU92
G	ARG199
H	GLU92
H	ARG199
A	ARG199
B	GLU92
B	ARG199
C	GLU92
C	ARG199
D	GLU92
D	ARG199
E	GLU92

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