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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 Residues16
DetailsACT_SITE: Involved in ionization of N3 of dUMP, leading to its activation => ECO:0000250|UniProtKB:Q9WYT0
ChainResidueDetails
AARG182
JARG182
KARG182
LARG182
MARG182
NARG182
OARG182
PARG182
BARG182
CARG182
DARG182
EARG182
FARG182
GARG182
HARG182
IARG182

site_idSWS_FT_FI2
Number of Residues96
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:Q9WYT0
ChainResidueDetails
ASER55
BGLU86
BHIS177
BARG182
CSER55
CGLN75
CARG78
CGLU86
CHIS177
CARG182
DSER55
AGLN75
DGLN75
DARG78
DGLU86
DHIS177
DARG182
ESER55
EGLN75
EARG78
EGLU86
EHIS177
AARG78
EARG182
FSER55
FGLN75
FARG78
FGLU86
FHIS177
FARG182
GSER55
GGLN75
GARG78
AGLU86
GGLU86
GHIS177
GARG182
HSER55
HGLN75
HARG78
HGLU86
HHIS177
HARG182
ISER55
AHIS177
IGLN75
IARG78
IGLU86
IHIS177
IARG182
JSER55
JGLN75
JARG78
JGLU86
JHIS177
AARG182
JARG182
KSER55
KGLN75
KARG78
KGLU86
KHIS177
KARG182
LSER55
LGLN75
LARG78
BSER55
LGLU86
LHIS177
LARG182
MSER55
MGLN75
MARG78
MGLU86
MHIS177
MARG182
NSER55
BGLN75
NGLN75
NARG78
NGLU86
NHIS177
NARG182
OSER55
OGLN75
OARG78
OGLU86
OHIS177
BARG78
OARG182
PSER55
PGLN75
PARG78
PGLU86
PHIS177
PARG182

site_idSWS_FT_FI3
Number of Residues16
DetailsBINDING: in other chain => ECO:0000250|UniProtKB:Q9WYT0
ChainResidueDetails
AARG155
JARG155
KARG155
LARG155
MARG155
NARG155
OARG155
PARG155
BARG155
CARG155
DARG155
EARG155
FARG155
GARG155
HARG155
IARG155

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PDB entries from 2024-07-10

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