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4EB4

Crystal structure of mouse thymidylate synthase in ternary complex with dUMP and Tomudex

Functional Information from GO Data
ChainGOidnamespacecontents
A0000900molecular_functionmRNA regulatory element binding translation repressor activity
A0003729molecular_functionmRNA binding
A0004799molecular_functionthymidylate synthase activity
A0005542molecular_functionfolic acid binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005743cellular_componentmitochondrial inner membrane
A0005759cellular_componentmitochondrial matrix
A0006206biological_processpyrimidine nucleobase metabolic process
A0006231biological_processdTMP biosynthetic process
A0006235biological_processdTTP biosynthetic process
A0006417biological_processregulation of translation
A0007623biological_processcircadian rhythm
A0008168molecular_functionmethyltransferase activity
A0009165biological_processnucleotide biosynthetic process
A0009410biological_processresponse to xenobiotic stimulus
A0009636biological_processresponse to toxic substance
A0014070biological_processresponse to organic cyclic compound
A0016741molecular_functiontransferase activity, transferring one-carbon groups
A0017148biological_processnegative regulation of translation
A0019860biological_processuracil metabolic process
A0032259biological_processmethylation
A0032570biological_processresponse to progesterone
A0033189biological_processresponse to vitamin A
A0034097biological_processresponse to cytokine
A0035999biological_processtetrahydrofolate interconversion
A0042803molecular_functionprotein homodimerization activity
A0045471biological_processresponse to ethanol
A0046653biological_processtetrahydrofolate metabolic process
A0046683biological_processresponse to organophosphorus
A0048589biological_processdevelopmental growth
A0051216biological_processcartilage development
A0051384biological_processresponse to glucocorticoid
A0051593biological_processresponse to folic acid
A0060574biological_processintestinal epithelial cell maturation
A0097421biological_processliver regeneration
A1901363molecular_functionheterocyclic compound binding
A1990825molecular_functionsequence-specific mRNA binding
B0000900molecular_functionmRNA regulatory element binding translation repressor activity
B0003729molecular_functionmRNA binding
B0004799molecular_functionthymidylate synthase activity
B0005542molecular_functionfolic acid binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005743cellular_componentmitochondrial inner membrane
B0005759cellular_componentmitochondrial matrix
B0006206biological_processpyrimidine nucleobase metabolic process
B0006231biological_processdTMP biosynthetic process
B0006235biological_processdTTP biosynthetic process
B0006417biological_processregulation of translation
B0007623biological_processcircadian rhythm
B0008168molecular_functionmethyltransferase activity
B0009165biological_processnucleotide biosynthetic process
B0009410biological_processresponse to xenobiotic stimulus
B0009636biological_processresponse to toxic substance
B0014070biological_processresponse to organic cyclic compound
B0016741molecular_functiontransferase activity, transferring one-carbon groups
B0017148biological_processnegative regulation of translation
B0019860biological_processuracil metabolic process
B0032259biological_processmethylation
B0032570biological_processresponse to progesterone
B0033189biological_processresponse to vitamin A
B0034097biological_processresponse to cytokine
B0035999biological_processtetrahydrofolate interconversion
B0042803molecular_functionprotein homodimerization activity
B0045471biological_processresponse to ethanol
B0046653biological_processtetrahydrofolate metabolic process
B0046683biological_processresponse to organophosphorus
B0048589biological_processdevelopmental growth
B0051216biological_processcartilage development
B0051384biological_processresponse to glucocorticoid
B0051593biological_processresponse to folic acid
B0060574biological_processintestinal epithelial cell maturation
B0097421biological_processliver regeneration
B1901363molecular_functionheterocyclic compound binding
B1990825molecular_functionsequence-specific mRNA binding
C0000900molecular_functionmRNA regulatory element binding translation repressor activity
C0003729molecular_functionmRNA binding
C0004799molecular_functionthymidylate synthase activity
C0005542molecular_functionfolic acid binding
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005739cellular_componentmitochondrion
C0005743cellular_componentmitochondrial inner membrane
C0005759cellular_componentmitochondrial matrix
C0006206biological_processpyrimidine nucleobase metabolic process
C0006231biological_processdTMP biosynthetic process
C0006235biological_processdTTP biosynthetic process
C0006417biological_processregulation of translation
C0007623biological_processcircadian rhythm
C0008168molecular_functionmethyltransferase activity
C0009165biological_processnucleotide biosynthetic process
C0009410biological_processresponse to xenobiotic stimulus
C0009636biological_processresponse to toxic substance
C0014070biological_processresponse to organic cyclic compound
C0016741molecular_functiontransferase activity, transferring one-carbon groups
C0017148biological_processnegative regulation of translation
C0019860biological_processuracil metabolic process
C0032259biological_processmethylation
C0032570biological_processresponse to progesterone
C0033189biological_processresponse to vitamin A
C0034097biological_processresponse to cytokine
C0035999biological_processtetrahydrofolate interconversion
C0042803molecular_functionprotein homodimerization activity
C0045471biological_processresponse to ethanol
C0046653biological_processtetrahydrofolate metabolic process
C0046683biological_processresponse to organophosphorus
C0048589biological_processdevelopmental growth
C0051216biological_processcartilage development
C0051384biological_processresponse to glucocorticoid
C0051593biological_processresponse to folic acid
C0060574biological_processintestinal epithelial cell maturation
C0097421biological_processliver regeneration
C1901363molecular_functionheterocyclic compound binding
C1990825molecular_functionsequence-specific mRNA binding
D0000900molecular_functionmRNA regulatory element binding translation repressor activity
D0003729molecular_functionmRNA binding
D0004799molecular_functionthymidylate synthase activity
D0005542molecular_functionfolic acid binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005739cellular_componentmitochondrion
D0005743cellular_componentmitochondrial inner membrane
D0005759cellular_componentmitochondrial matrix
D0006206biological_processpyrimidine nucleobase metabolic process
D0006231biological_processdTMP biosynthetic process
D0006235biological_processdTTP biosynthetic process
D0006417biological_processregulation of translation
D0007623biological_processcircadian rhythm
D0008168molecular_functionmethyltransferase activity
D0009165biological_processnucleotide biosynthetic process
D0009410biological_processresponse to xenobiotic stimulus
D0009636biological_processresponse to toxic substance
D0014070biological_processresponse to organic cyclic compound
D0016741molecular_functiontransferase activity, transferring one-carbon groups
D0017148biological_processnegative regulation of translation
D0019860biological_processuracil metabolic process
D0032259biological_processmethylation
D0032570biological_processresponse to progesterone
D0033189biological_processresponse to vitamin A
D0034097biological_processresponse to cytokine
D0035999biological_processtetrahydrofolate interconversion
D0042803molecular_functionprotein homodimerization activity
D0045471biological_processresponse to ethanol
D0046653biological_processtetrahydrofolate metabolic process
D0046683biological_processresponse to organophosphorus
D0048589biological_processdevelopmental growth
D0051216biological_processcartilage development
D0051384biological_processresponse to glucocorticoid
D0051593biological_processresponse to folic acid
D0060574biological_processintestinal epithelial cell maturation
D0097421biological_processliver regeneration
D1901363molecular_functionheterocyclic compound binding
D1990825molecular_functionsequence-specific mRNA binding
Functional Information from PDB Data
site_idAC1
Number of Residues16
DetailsBINDING SITE FOR RESIDUE UMP A 401
ChainResidue
AARG44
AHIS250
ATYR252
AD16402
AHOH502
AHOH625
BARG169
BARG170
ACYS189
AHIS190
AGLN208
AARG209
ASER210
AGLY211
AASP212
AASN220

site_idAC2
Number of Residues21
DetailsBINDING SITE FOR RESIDUE D16 A 402
ChainResidue
APHE74
AILE102
ATRP103
AASP212
ALEU215
AGLY216
APHE219
AASN220
ATYR252
ALYS302
AMET303
AMET305
AALA306
AUMP401
AHOH517
AHOH635
AHOH665
AHOH684
AHOH746
AHOH855
AHOH893

site_idAC3
Number of Residues12
DetailsBINDING SITE FOR RESIDUE DTT A 403
ChainResidue
AGLN154
ALYS157
AVAL158
ATHR161
AASP168
AARG170
AILE172
AHOH550
AHOH562
AHOH631
AHOH793
BLEU181

site_idAC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL A 404
ChainResidue
AASP167
AVAL198
AASN199
AHOH645
AHOH767
BLYS40
BLYS41
BGLU42

site_idAC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL A 405
ChainResidue
AASN177
ALYS179
AHOH702
AHOH853
BGLY137
BASN177
BLYS179

site_idAC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE GOL A 406
ChainResidue
AHOH618
AHOH628

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL A 407
ChainResidue
AARG277
ALYS278
AHOH797
BLYS87
BLYS98

site_idAC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 A 408
ChainResidue
AARG268
APRO297
AHIS298
APRO299

site_idAC9
Number of Residues15
DetailsBINDING SITE FOR RESIDUE UMP B 401
ChainResidue
AARG169
AARG170
BARG44
BCYS189
BHIS190
BGLN208
BARG209
BSER210
BASP212
BASN220
BHIS250
BTYR252
BD16402
BHOH595
BHOH838

site_idBC1
Number of Residues21
DetailsBINDING SITE FOR RESIDUE D16 B 402
ChainResidue
BLYS302
BMET303
BMET305
BALA306
BUMP401
BHOH570
BHOH612
BHOH679
BHOH680
BHOH715
BHOH774
BHOH832
BPHE74
BILE102
BTRP103
BASN106
BASP212
BLEU215
BGLY216
BPHE219
BTYR252

site_idBC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE GOL B 403
ChainResidue
BLEU115
BLEU181
BPRO182
BMET184
BPRO187
BHOH512
BHOH532
BHOH738
BHOH796
BHOH846

site_idBC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL B 404
ChainResidue
ALYS40
ALYS41
AGLU42
AHOH741
BASP167
BVAL198
BASN199
BHOH740

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL B 405
ChainResidue
BHIS22
BGLU24
BLEU25
BPRO269
BHOH566

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MES B 406
ChainResidue
BARG36
BCYS37
BGLY38
BPHE39
BLYS40
BHOH843

site_idBC6
Number of Residues15
DetailsBINDING SITE FOR RESIDUE UMP C 401
ChainResidue
CARG44
CCYS189
CHIS190
CARG209
CSER210
CASP212
CGLY216
CASN220
CHIS250
CTYR252
CD16402
CHOH505
CHOH694
DARG169
DARG170

site_idBC7
Number of Residues13
DetailsBINDING SITE FOR RESIDUE D16 C 402
ChainResidue
CPHE74
CARG101
CASP212
CLEU215
CGLY216
CPHE219
CTYR252
CUMP401
CHOH564
CHOH618
CHOH622
CHOH680
CHOH741

site_idBC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL C 403
ChainResidue
CARG21
CARG58
CHOH606
CHOH754

site_idBC9
Number of Residues15
DetailsBINDING SITE FOR RESIDUE UMP D 401
ChainResidue
CARG169
CARG170
DARG44
DCYS189
DHIS190
DARG209
DSER210
DGLY211
DASP212
DGLY216
DASN220
DHIS250
DTYR252
DD16402
DHOH566

site_idCC1
Number of Residues13
DetailsBINDING SITE FOR RESIDUE D16 D 402
ChainResidue
DPHE74
DILE102
DASP212
DLEU215
DGLY216
DPHE219
DTYR252
DLYS302
DMET303
DUMP401
DHOH603
DHOH686
DHOH699

site_idCC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL D 403
ChainResidue
DARG36
DCYS37
DGLY38
DPHE39
DGOL404

site_idCC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL D 404
ChainResidue
CASN199
DPHE39
DLYS40
DGOL403

Functional Information from PROSITE/UniProt
site_idPS00091
Number of Residues29
DetailsTHYMIDYLATE_SYNTHASE Thymidylate synthase active site. RriImcaWNpkdlplma.....LpPCHalcQFyV
ChainResidueDetails
AARG169-VAL197

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE: Nucleophile => ECO:0000250|UniProtKB:P0A884
ChainResidueDetails
ACYS189
BCYS189
CCYS189
DCYS189

site_idSWS_FT_FI2
Number of Residues8
DetailsBINDING: in other chain => ECO:0000250|UniProtKB:P0A884
ChainResidueDetails
AARG44
AASN220
BARG44
BASN220
CARG44
CASN220
DARG44
DASN220

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P45352
ChainResidueDetails
AARG169
BARG169
CARG169
DARG169

site_idSWS_FT_FI4
Number of Residues12
DetailsBINDING: in other chain => ECO:0000250|UniProtKB:P45352
ChainResidueDetails
ACYS189
DCYS189
DARG209
DHIS250
AARG209
AHIS250
BCYS189
BARG209
BHIS250
CCYS189
CARG209
CHIS250

site_idSWS_FT_FI5
Number of Residues8
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P0A884
ChainResidueDetails
AASP212
AALA306
BASP212
BALA306
CASP212
CALA306
DASP212
DALA306

site_idSWS_FT_FI6
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P04818
ChainResidueDetails
ASER108
BSER108
CSER108
DSER108

site_idSWS_FT_FI7
Number of Residues12
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0000250|UniProtKB:P04818
ChainResidueDetails
ALYS286
DLYS286
DLYS302
ALYS302
BLYS286
BLYS302
CLYS286
CLYS302

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PDB entries from 2024-12-25

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