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4FZB

Structure of thymidylate synthase ThyX complexed to a new inhibitor

Functional Information from GO Data
ChainGOidnamespacecontents
A0004799molecular_functionthymidylate synthase activity
A0006231biological_processdTMP biosynthetic process
A0006235biological_processdTTP biosynthetic process
A0008168molecular_functionmethyltransferase activity
A0009165biological_processnucleotide biosynthetic process
A0016740molecular_functiontransferase activity
A0032259biological_processmethylation
A0050660molecular_functionflavin adenine dinucleotide binding
A0050797molecular_functionthymidylate synthase (FAD) activity
A0070402molecular_functionNADPH binding
B0004799molecular_functionthymidylate synthase activity
B0006231biological_processdTMP biosynthetic process
B0006235biological_processdTTP biosynthetic process
B0008168molecular_functionmethyltransferase activity
B0009165biological_processnucleotide biosynthetic process
B0016740molecular_functiontransferase activity
B0032259biological_processmethylation
B0050660molecular_functionflavin adenine dinucleotide binding
B0050797molecular_functionthymidylate synthase (FAD) activity
B0070402molecular_functionNADPH binding
C0004799molecular_functionthymidylate synthase activity
C0006231biological_processdTMP biosynthetic process
C0006235biological_processdTTP biosynthetic process
C0008168molecular_functionmethyltransferase activity
C0009165biological_processnucleotide biosynthetic process
C0016740molecular_functiontransferase activity
C0032259biological_processmethylation
C0050660molecular_functionflavin adenine dinucleotide binding
C0050797molecular_functionthymidylate synthase (FAD) activity
C0070402molecular_functionNADPH binding
D0004799molecular_functionthymidylate synthase activity
D0006231biological_processdTMP biosynthetic process
D0006235biological_processdTTP biosynthetic process
D0008168molecular_functionmethyltransferase activity
D0009165biological_processnucleotide biosynthetic process
D0016740molecular_functiontransferase activity
D0032259biological_processmethylation
D0050660molecular_functionflavin adenine dinucleotide binding
D0050797molecular_functionthymidylate synthase (FAD) activity
D0070402molecular_functionNADPH binding
E0004799molecular_functionthymidylate synthase activity
E0006231biological_processdTMP biosynthetic process
E0006235biological_processdTTP biosynthetic process
E0008168molecular_functionmethyltransferase activity
E0009165biological_processnucleotide biosynthetic process
E0016740molecular_functiontransferase activity
E0032259biological_processmethylation
E0050660molecular_functionflavin adenine dinucleotide binding
E0050797molecular_functionthymidylate synthase (FAD) activity
E0070402molecular_functionNADPH binding
F0004799molecular_functionthymidylate synthase activity
F0006231biological_processdTMP biosynthetic process
F0006235biological_processdTTP biosynthetic process
F0008168molecular_functionmethyltransferase activity
F0009165biological_processnucleotide biosynthetic process
F0016740molecular_functiontransferase activity
F0032259biological_processmethylation
F0050660molecular_functionflavin adenine dinucleotide binding
F0050797molecular_functionthymidylate synthase (FAD) activity
F0070402molecular_functionNADPH binding
G0004799molecular_functionthymidylate synthase activity
G0006231biological_processdTMP biosynthetic process
G0006235biological_processdTTP biosynthetic process
G0008168molecular_functionmethyltransferase activity
G0009165biological_processnucleotide biosynthetic process
G0016740molecular_functiontransferase activity
G0032259biological_processmethylation
G0050660molecular_functionflavin adenine dinucleotide binding
G0050797molecular_functionthymidylate synthase (FAD) activity
G0070402molecular_functionNADPH binding
H0004799molecular_functionthymidylate synthase activity
H0006231biological_processdTMP biosynthetic process
H0006235biological_processdTTP biosynthetic process
H0008168molecular_functionmethyltransferase activity
H0009165biological_processnucleotide biosynthetic process
H0016740molecular_functiontransferase activity
H0032259biological_processmethylation
H0050660molecular_functionflavin adenine dinucleotide binding
H0050797molecular_functionthymidylate synthase (FAD) activity
H0070402molecular_functionNADPH binding
I0004799molecular_functionthymidylate synthase activity
I0006231biological_processdTMP biosynthetic process
I0006235biological_processdTTP biosynthetic process
I0008168molecular_functionmethyltransferase activity
I0009165biological_processnucleotide biosynthetic process
I0016740molecular_functiontransferase activity
I0032259biological_processmethylation
I0050660molecular_functionflavin adenine dinucleotide binding
I0050797molecular_functionthymidylate synthase (FAD) activity
I0070402molecular_functionNADPH binding
J0004799molecular_functionthymidylate synthase activity
J0006231biological_processdTMP biosynthetic process
J0006235biological_processdTTP biosynthetic process
J0008168molecular_functionmethyltransferase activity
J0009165biological_processnucleotide biosynthetic process
J0016740molecular_functiontransferase activity
J0032259biological_processmethylation
J0050660molecular_functionflavin adenine dinucleotide binding
J0050797molecular_functionthymidylate synthase (FAD) activity
J0070402molecular_functionNADPH binding
K0004799molecular_functionthymidylate synthase activity
K0006231biological_processdTMP biosynthetic process
K0006235biological_processdTTP biosynthetic process
K0008168molecular_functionmethyltransferase activity
K0009165biological_processnucleotide biosynthetic process
K0016740molecular_functiontransferase activity
K0032259biological_processmethylation
K0050660molecular_functionflavin adenine dinucleotide binding
K0050797molecular_functionthymidylate synthase (FAD) activity
K0070402molecular_functionNADPH binding
L0004799molecular_functionthymidylate synthase activity
L0006231biological_processdTMP biosynthetic process
L0006235biological_processdTTP biosynthetic process
L0008168molecular_functionmethyltransferase activity
L0009165biological_processnucleotide biosynthetic process
L0016740molecular_functiontransferase activity
L0032259biological_processmethylation
L0050660molecular_functionflavin adenine dinucleotide binding
L0050797molecular_functionthymidylate synthase (FAD) activity
L0070402molecular_functionNADPH binding
M0004799molecular_functionthymidylate synthase activity
M0006231biological_processdTMP biosynthetic process
M0006235biological_processdTTP biosynthetic process
M0008168molecular_functionmethyltransferase activity
M0009165biological_processnucleotide biosynthetic process
M0016740molecular_functiontransferase activity
M0032259biological_processmethylation
M0050660molecular_functionflavin adenine dinucleotide binding
M0050797molecular_functionthymidylate synthase (FAD) activity
M0070402molecular_functionNADPH binding
N0004799molecular_functionthymidylate synthase activity
N0006231biological_processdTMP biosynthetic process
N0006235biological_processdTTP biosynthetic process
N0008168molecular_functionmethyltransferase activity
N0009165biological_processnucleotide biosynthetic process
N0016740molecular_functiontransferase activity
N0032259biological_processmethylation
N0050660molecular_functionflavin adenine dinucleotide binding
N0050797molecular_functionthymidylate synthase (FAD) activity
N0070402molecular_functionNADPH binding
O0004799molecular_functionthymidylate synthase activity
O0006231biological_processdTMP biosynthetic process
O0006235biological_processdTTP biosynthetic process
O0008168molecular_functionmethyltransferase activity
O0009165biological_processnucleotide biosynthetic process
O0016740molecular_functiontransferase activity
O0032259biological_processmethylation
O0050660molecular_functionflavin adenine dinucleotide binding
O0050797molecular_functionthymidylate synthase (FAD) activity
O0070402molecular_functionNADPH binding
P0004799molecular_functionthymidylate synthase activity
P0006231biological_processdTMP biosynthetic process
P0006235biological_processdTTP biosynthetic process
P0008168molecular_functionmethyltransferase activity
P0009165biological_processnucleotide biosynthetic process
P0016740molecular_functiontransferase activity
P0032259biological_processmethylation
P0050660molecular_functionflavin adenine dinucleotide binding
P0050797molecular_functionthymidylate synthase (FAD) activity
P0070402molecular_functionNADPH binding
Functional Information from PDB Data
site_idAC1
Number of Residues25
DetailsBINDING SITE FOR RESIDUE FAD A 301
ChainResidue
ATRP54
AARG182
AFAD302
A0VJ303
AHOH402
AHOH403
CGLN85
CGLU86
CSER88
DSER30
DASN31
AARG78
DHIS51
DHIS53
DTRP54
DSER55
DGLU58
DARG173
AHIS79
AARG80
ASER81
AARG173
AASP174
AHIS177
ALEU181

site_idAC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE FAD A 302
ChainResidue
AASN31
AHIS51
AHIS53
ATRP54
ASER55
AARG173
AFAD301
AHOH407
BGLN85
BGLU86
BSER88
B0VJ303
DARG78
DHIS79
DARG80
DSER81
DARG173
DASP174
DHIS177
DARG182

site_idAC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 0VJ A 303
ChainResidue
AGLN75
AARG78
AARG182
AGLY186
AGLN188
AFAD301
CGLU86
CPHE87
CSER88
CGLN89
CARG90

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS A 304
ChainResidue
AGLN85
APHE87
ATHR165
ATYR167
BVAL29

site_idAC5
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ A 305
ChainResidue
AGLU86
APHE87
ASER88
AGLN89
AARG90
AGLU152
CGLN75
CARG78
CARG182
CGLY186
CGLN188
CFAD301

site_idAC6
Number of Residues20
DetailsBINDING SITE FOR RESIDUE FAD B 301
ChainResidue
BTRP54
BARG78
BHIS79
BARG80
BSER81
BARG173
BASP174
BHIS177
BARG182
CSER30
CASN31
CHIS53
CTRP54
CSER55
CARG173
CFAD301
DGLN85
DGLU86
DSER88
D0VJ301

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS B 302
ChainResidue
BGLN85
BPHE87
BTHR165
BILE166
BTYR167

site_idAC8
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 0VJ B 303
ChainResidue
BPHE87
BSER88
BGLN89
BARG90
BGLU152
DGLN75
DARG78
DARG182
DGLY186
DGLN188
AFAD302

site_idAC9
Number of Residues19
DetailsBINDING SITE FOR RESIDUE FAD C 301
ChainResidue
AGLN85
AGLU86
ASER88
A0VJ305
BSER30
BHIS51
BHIS53
BTRP54
BSER55
BARG173
BFAD301
CTRP54
CARG78
CHIS79
CARG80
CSER81
CARG173
CASP174
CHIS177

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS C 302
ChainResidue
CGLN85
CGLU86
CPHE87
CTHR165
DVAL29

site_idBC2
Number of Residues13
DetailsBINDING SITE FOR RESIDUE 0VJ D 301
ChainResidue
BALA74
BGLN75
BARG78
BARG182
BGLY186
BGLN188
BFAD301
DGLU86
DPHE87
DSER88
DGLN89
DARG90
DGLU152

site_idBC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE DMS D 302
ChainResidue
CVAL29
CSER30
DGLN85
DGLU86
DPHE87
DTHR165
DTYR167

site_idBC4
Number of Residues20
DetailsBINDING SITE FOR RESIDUE FAD E 301
ChainResidue
ETRP54
EARG78
EHIS79
EARG80
ESER81
EARG173
EASP174
EHIS177
EARG182
E0VJ302
GGLN85
GGLU86
GSER88
HSER30
HHIS51
HHIS53
HTRP54
HSER55
HARG173
HFAD302

site_idBC5
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ E 302
ChainResidue
EGLN75
EARG78
EARG182
EGLY186
EGLN188
EFAD301
GGLU86
GPHE87
GSER88
GGLN89
GARG90
GGLU152

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS E 303
ChainResidue
EGLN85
EGLU86
EPHE87
ETHR165
ETYR167

site_idBC7
Number of Residues22
DetailsBINDING SITE FOR RESIDUE FAD F 301
ChainResidue
FARG78
FHIS79
FARG80
FSER81
FARG173
FASP174
FHIS177
FLEU181
FARG182
FFAD302
FHOH412
GASN31
GHIS51
GHIS53
GTRP54
GSER55
GARG173
GHOH410
HGLN85
HGLU86
HSER88
H0VJ301

site_idBC8
Number of Residues19
DetailsBINDING SITE FOR RESIDUE FAD F 302
ChainResidue
EGLN85
EGLU86
FASN31
FHIS51
FHIS53
FTRP54
FSER55
FARG173
FFAD301
GTRP54
GARG78
GHIS79
GARG80
GSER81
GARG173
GASP174
GHIS177
GLEU181
G0VJ301

site_idBC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS F 303
ChainResidue
EVAL29
FGLN85
FGLU86
FPHE87
FTHR165
FTYR167

site_idCC1
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 0VJ F 304
ChainResidue
FGLU86
FPHE87
FSER88
FGLN89
FARG90
FGLU152
HGLN75
HARG182
HGLY186
HGLN188
HFAD302

site_idCC2
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 0VJ G 301
ChainResidue
EGLU86
EPHE87
ESER88
EGLN89
EARG90
FFAD302
GGLN75
GARG78
GARG182
GGLY186
GGLN188

site_idCC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE DMS G 302
ChainResidue
GGLN85
GTHR165
HVAL29

site_idCC4
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ H 301
ChainResidue
FGLN75
FARG78
FARG182
FGLY186
FGLN188
FFAD301
HGLU86
HPHE87
HSER88
HGLN89
HARG90
HGLU152

site_idCC5
Number of Residues23
DetailsBINDING SITE FOR RESIDUE FAD H 302
ChainResidue
ESER30
EASN31
EHIS51
EHIS53
ETRP54
ESER55
EARG173
EFAD301
FGLN85
FGLU86
FSER88
F0VJ304
HTRP54
HARG78
HHIS79
HARG80
HSER81
HARG173
HASP174
HHIS177
HLEU181
HARG182
HHOH405

site_idCC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE DMS H 303
ChainResidue
HGLN85
HPHE87
HTHR165
HTYR167

site_idCC7
Number of Residues22
DetailsBINDING SITE FOR RESIDUE FAD I 301
ChainResidue
ITRP54
IARG78
IHIS79
IARG80
ISER81
IARG173
IASP174
IHIS177
IARG182
IFAD302
IHOH402
KGLN85
KGLU86
KSER88
K0VJ301
LASN31
LHIS51
LHIS53
LTRP54
LSER55
LARG173
LHOH401

site_idCC8
Number of Residues21
DetailsBINDING SITE FOR RESIDUE FAD I 302
ChainResidue
ISER30
IHIS51
IHIS53
ITRP54
ISER55
IARG173
IFAD301
JGLN85
JGLU86
JSER88
LTRP54
LARG78
LHIS79
LARG80
LSER81
LARG173
LASP174
LHIS177
LARG182
L0VJ301
LHOH406

site_idCC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS I 303
ChainResidue
IGLN85
ITHR165
IILE166
ITYR167
JVAL29

site_idDC1
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 0VJ I 304
ChainResidue
IGLU86
IPHE87
ISER88
IGLN89
IARG90
IGLU152
KARG78
KARG182
KGLY186
KGLN188
KFAD302

site_idDC2
Number of Residues22
DetailsBINDING SITE FOR RESIDUE FAD J 301
ChainResidue
JTRP54
JARG78
JHIS79
JARG80
JSER81
JARG173
JASP174
JHIS177
JLEU181
JARG182
J0VJ302
KASN31
KHIS51
KLYS52
KHIS53
KTRP54
KSER55
KARG173
KFAD302
LGLN85
LGLU86
LSER88

site_idDC3
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ J 302
ChainResidue
JGLN75
JARG78
JARG182
JGLY186
JGLN188
JFAD301
LGLU86
LPHE87
LSER88
LGLN89
LARG90
LGLU152

site_idDC4
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 0VJ K 301
ChainResidue
IARG78
IARG182
IGLY186
IGLN188
IFAD301
KGLU86
KPHE87
KSER88
KGLN89
KARG90
KGLU152

site_idDC5
Number of Residues21
DetailsBINDING SITE FOR RESIDUE FAD K 302
ChainResidue
IGLN85
IGLU86
ISER88
I0VJ304
JSER30
JHIS51
JHIS53
JTRP54
JSER55
JARG173
JFAD301
JHOH405
KTRP54
KARG78
KHIS79
KARG80
KSER81
KARG173
KASP174
KHIS177
KARG182

site_idDC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS K 303
ChainResidue
KGLN85
KGLU86
KPHE87
KTHR165
KTYR167
LSER30

site_idDC7
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ L 301
ChainResidue
IFAD302
JGLU86
JPHE87
JSER88
JGLN89
JARG90
JGLU152
LGLN75
LARG78
LARG182
LGLY186
LGLN188

site_idDC8
Number of Residues20
DetailsBINDING SITE FOR RESIDUE FAD M 301
ChainResidue
MTRP54
MARG78
MHIS79
MARG80
MSER81
MARG173
MASP174
MHIS177
MARG182
OGLN85
OGLU86
OSER88
O0VJ301
PASN31
PHIS51
PHIS53
PTRP54
PSER55
PARG173
PFAD301

site_idDC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS M 302
ChainResidue
MGLN85
MGLU86
MTHR165
MILE166
MTYR167

site_idEC1
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ M 303
ChainResidue
MGLU86
MPHE87
MSER88
MGLN89
MARG90
MGLU152
OGLN75
OARG78
OARG182
OGLY186
OGLN188
OFAD302

site_idEC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE FAD N 301
ChainResidue
NTRP54
NARG78
NHIS79
NARG80
NSER81
NARG173
NASP174
NHIS177
NLEU181
N0VJ302
OASN31
OHIS51
OHIS53
OTRP54
OSER55
OARG173
OFAD302
PGLN85
PGLU86
PSER88

site_idEC3
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ N 302
ChainResidue
NGLN75
NARG78
NARG182
NGLY186
NGLN188
NFAD301
PGLU86
PPHE87
PSER88
PGLN89
PARG90
PGLU152

site_idEC4
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ O 301
ChainResidue
MGLN75
MARG78
MARG182
MGLY186
MGLN188
MFAD301
OGLU86
OPHE87
OSER88
OGLN89
OARG90
OGLU152

site_idEC5
Number of Residues19
DetailsBINDING SITE FOR RESIDUE FAD O 302
ChainResidue
MGLN85
MGLU86
MSER88
M0VJ303
NSER30
NHIS51
NHIS53
NTRP54
NSER55
NARG173
NFAD301
OARG78
OHIS79
OSER81
OARG173
OASP174
OHIS177
OLEU181
OARG182

site_idEC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS O 303
ChainResidue
OGLN85
OPHE87
OTHR165
OTYR167
PVAL29
PSER30

site_idEC7
Number of Residues20
DetailsBINDING SITE FOR RESIDUE FAD P 301
ChainResidue
MSER30
MHIS51
MHIS53
MTRP54
MSER55
MARG173
MFAD301
NGLN85
NGLU86
NSER88
PTRP54
PARG78
PHIS79
PARG80
PSER81
PARG173
PASP174
PHIS177
PARG182
P0VJ302

site_idEC8
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0VJ P 302
ChainResidue
NGLU86
NPHE87
NSER88
NGLN89
NARG90
NGLU152
PGLN75
PARG78
PARG182
PGLY186
PGLN188
PFAD301

site_idEC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS P 303
ChainResidue
OSER30
PGLN85
PPHE87
PTHR165
PTYR167

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues160
DetailsMotif: {"description":"ThyX motif","evidences":[{"source":"PROSITE-ProRule","id":"PRU00661","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues16
DetailsActive site: {"description":"Involved in ionization of N3 of dUMP, leading to its activation","evidences":[{"source":"UniProtKB","id":"Q9WYT0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues144
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"Q9WYT0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues80
DetailsBinding site: {"description":"in other chain","evidences":[{"source":"UniProtKB","id":"Q9WYT0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

245011

PDB entries from 2025-11-19

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