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2VDC

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

Functional Information from GO Data
ChainGOidnamespacecontents
A0004355molecular_functionglutamate synthase (NADPH) activity
A0006537biological_processglutamate biosynthetic process
A0006541biological_processglutamine metabolic process
A0015930molecular_functionglutamate synthase activity
A0016491molecular_functionoxidoreductase activity
A0016638molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors
A0019676biological_processammonia assimilation cycle
A0046872molecular_functionmetal ion binding
A0051538molecular_function3 iron, 4 sulfur cluster binding
A0097054biological_processL-glutamate biosynthetic process
B0004355molecular_functionglutamate synthase (NADPH) activity
B0006537biological_processglutamate biosynthetic process
B0006541biological_processglutamine metabolic process
B0015930molecular_functionglutamate synthase activity
B0016491molecular_functionoxidoreductase activity
B0016638molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors
B0019676biological_processammonia assimilation cycle
B0046872molecular_functionmetal ion binding
B0051538molecular_function3 iron, 4 sulfur cluster binding
B0097054biological_processL-glutamate biosynthetic process
C0004355molecular_functionglutamate synthase (NADPH) activity
C0006537biological_processglutamate biosynthetic process
C0006541biological_processglutamine metabolic process
C0015930molecular_functionglutamate synthase activity
C0016491molecular_functionoxidoreductase activity
C0016638molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors
C0019676biological_processammonia assimilation cycle
C0046872molecular_functionmetal ion binding
C0051538molecular_function3 iron, 4 sulfur cluster binding
C0097054biological_processL-glutamate biosynthetic process
D0004355molecular_functionglutamate synthase (NADPH) activity
D0006537biological_processglutamate biosynthetic process
D0006541biological_processglutamine metabolic process
D0015930molecular_functionglutamate synthase activity
D0016491molecular_functionoxidoreductase activity
D0016638molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors
D0019676biological_processammonia assimilation cycle
D0046872molecular_functionmetal ion binding
D0051538molecular_function3 iron, 4 sulfur cluster binding
D0097054biological_processL-glutamate biosynthetic process
E0004355molecular_functionglutamate synthase (NADPH) activity
E0006537biological_processglutamate biosynthetic process
E0006541biological_processglutamine metabolic process
E0015930molecular_functionglutamate synthase activity
E0016491molecular_functionoxidoreductase activity
E0016638molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors
E0019676biological_processammonia assimilation cycle
E0046872molecular_functionmetal ion binding
E0051538molecular_function3 iron, 4 sulfur cluster binding
E0097054biological_processL-glutamate biosynthetic process
F0004355molecular_functionglutamate synthase (NADPH) activity
F0006537biological_processglutamate biosynthetic process
F0006541biological_processglutamine metabolic process
F0015930molecular_functionglutamate synthase activity
F0016491molecular_functionoxidoreductase activity
F0016638molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors
F0019676biological_processammonia assimilation cycle
F0046872molecular_functionmetal ion binding
F0051538molecular_function3 iron, 4 sulfur cluster binding
F0097054biological_processL-glutamate biosynthetic process
G0004355molecular_functionglutamate synthase (NADPH) activity
G0006537biological_processglutamate biosynthetic process
G0016491molecular_functionoxidoreductase activity
G0046872molecular_functionmetal ion binding
G0051536molecular_functioniron-sulfur cluster binding
G0051539molecular_function4 iron, 4 sulfur cluster binding
G0097054biological_processL-glutamate biosynthetic process
H0004355molecular_functionglutamate synthase (NADPH) activity
H0006537biological_processglutamate biosynthetic process
H0016491molecular_functionoxidoreductase activity
H0046872molecular_functionmetal ion binding
H0051536molecular_functioniron-sulfur cluster binding
H0051539molecular_function4 iron, 4 sulfur cluster binding
H0097054biological_processL-glutamate biosynthetic process
I0004355molecular_functionglutamate synthase (NADPH) activity
I0006537biological_processglutamate biosynthetic process
I0016491molecular_functionoxidoreductase activity
I0046872molecular_functionmetal ion binding
I0051536molecular_functioniron-sulfur cluster binding
I0051539molecular_function4 iron, 4 sulfur cluster binding
I0097054biological_processL-glutamate biosynthetic process
J0004355molecular_functionglutamate synthase (NADPH) activity
J0006537biological_processglutamate biosynthetic process
J0016491molecular_functionoxidoreductase activity
J0046872molecular_functionmetal ion binding
J0051536molecular_functioniron-sulfur cluster binding
J0051539molecular_function4 iron, 4 sulfur cluster binding
J0097054biological_processL-glutamate biosynthetic process
K0004355molecular_functionglutamate synthase (NADPH) activity
K0006537biological_processglutamate biosynthetic process
K0016491molecular_functionoxidoreductase activity
K0046872molecular_functionmetal ion binding
K0051536molecular_functioniron-sulfur cluster binding
K0051539molecular_function4 iron, 4 sulfur cluster binding
K0097054biological_processL-glutamate biosynthetic process
L0004355molecular_functionglutamate synthase (NADPH) activity
L0006537biological_processglutamate biosynthetic process
L0016491molecular_functionoxidoreductase activity
L0046872molecular_functionmetal ion binding
L0051536molecular_functioniron-sulfur cluster binding
L0051539molecular_function4 iron, 4 sulfur cluster binding
L0097054biological_processL-glutamate biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues9
DetailsBINDING SITE FOR RESIDUE OMT A 2473
ChainResidue
ACYS1
AARG210
ATYR211
AGLN223
AASN231
AGLY232
AGLU233
AASP273
ASER274

site_idAC2
Number of Residues19
DetailsBINDING SITE FOR RESIDUE FMN A 2474
ChainResidue
APRO856
AGLY857
AMET858
ASER859
AGLY885
AGLU886
AGLN909
ALYS931
ALYS999
AGLY1028
AGLY1029
ATHR1030
AGLY1031
AASP1070
AGLY1071
AGLY1072
AGLY1093
ATHR1094
AAKG2475

site_idAC3
Number of Residues9
DetailsBINDING SITE FOR RESIDUE AKG A 2475
ChainResidue
ASER859
AGLN934
ALYS937
AGLY942
AGLN943
AARG957
ATHR1030
AGLY1031
AFMN2474

site_idAC4
Number of Residues10
DetailsBINDING SITE FOR RESIDUE F3S A 2476
ChainResidue
ACYS1102
AILE1103
AMET1104
AVAL1105
AARG1106
AGLN1107
ACYS1108
ACYS1113
AVAL1117
ACYS1118

site_idAC5
Number of Residues10
DetailsBINDING SITE FOR RESIDUE OMT B 2473
ChainResidue
BCYS1
BGLN209
BARG210
BTYR211
BGLN223
BASN231
BGLY232
BGLU233
BASP273
BSER274

site_idAC6
Number of Residues18
DetailsBINDING SITE FOR RESIDUE FMN B 2474
ChainResidue
BPRO856
BGLY857
BMET858
BSER859
BGLU886
BGLN909
BLYS931
BLYS999
BGLY1028
BGLY1029
BTHR1030
BGLY1031
BASP1070
BGLY1071
BGLY1072
BGLY1093
BTHR1094
BAKG2475

site_idAC7
Number of Residues10
DetailsBINDING SITE FOR RESIDUE AKG B 2475
ChainResidue
BSER859
BGLN934
BLYS937
BGLY942
BGLN943
BARG957
BTHR1030
BGLY1031
BALA1032
BFMN2474

site_idAC8
Number of Residues10
DetailsBINDING SITE FOR RESIDUE F3S B 2476
ChainResidue
BCYS1102
BILE1103
BMET1104
BVAL1105
BARG1106
BGLN1107
BCYS1108
BCYS1113
BVAL1117
BCYS1118

site_idAC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE OMT C 2473
ChainResidue
CASN231
CGLY232
CGLU233
CASP273
CSER274
CCYS1
CARG210
CTYR211
CGLN223

site_idBC1
Number of Residues19
DetailsBINDING SITE FOR RESIDUE FMN C 2474
ChainResidue
CPRO856
CGLY857
CMET858
CSER859
CGLY885
CGLU886
CGLN909
CLYS931
CLYS999
CGLY1028
CGLY1029
CTHR1030
CGLY1031
CASP1070
CGLY1071
CGLY1072
CGLY1093
CTHR1094
CAKG2475

site_idBC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE AKG C 2475
ChainResidue
CSER859
CGLN934
CLYS937
CGLY942
CGLN943
CARG957
CTHR1030
CGLY1031
CFMN2474

site_idBC3
Number of Residues10
DetailsBINDING SITE FOR RESIDUE F3S C 2476
ChainResidue
CCYS1102
CILE1103
CMET1104
CVAL1105
CARG1106
CGLN1107
CCYS1108
CCYS1113
CVAL1117
CCYS1118

site_idBC4
Number of Residues10
DetailsBINDING SITE FOR RESIDUE OMT D 2473
ChainResidue
DCYS1
DGLN209
DARG210
DTYR211
DGLN223
DASN231
DGLY232
DGLU233
DASP273
DSER274

site_idBC5
Number of Residues18
DetailsBINDING SITE FOR RESIDUE FMN D 2474
ChainResidue
DPRO856
DGLY857
DMET858
DSER859
DGLU886
DGLN909
DLYS931
DLYS999
DGLY1028
DGLY1029
DTHR1030
DGLY1031
DASP1070
DGLY1071
DGLY1072
DGLY1093
DTHR1094
DAKG2475

site_idBC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE AKG D 2475
ChainResidue
DSER859
DGLN934
DLYS937
DGLY942
DGLN943
DARG957
DTHR1030
DGLY1031
DALA1032
DFMN2474

site_idBC7
Number of Residues10
DetailsBINDING SITE FOR RESIDUE F3S D 2476
ChainResidue
DCYS1102
DILE1103
DMET1104
DVAL1105
DARG1106
DGLN1107
DCYS1108
DCYS1113
DVAL1117
DCYS1118

site_idBC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE OMT E 2473
ChainResidue
ECYS1
EARG210
ETYR211
EGLN223
EASN231
EGLY232
EGLU233
EASP273
ESER274

site_idBC9
Number of Residues19
DetailsBINDING SITE FOR RESIDUE FMN E 2474
ChainResidue
EPRO856
EGLY857
EMET858
ESER859
EGLY885
EGLU886
EGLN909
ELYS931
ELYS999
EGLY1028
EGLY1029
ETHR1030
EGLY1031
EASP1070
EGLY1071
EGLY1072
EGLY1093
ETHR1094
EAKG2475

site_idCC1
Number of Residues9
DetailsBINDING SITE FOR RESIDUE AKG E 2475
ChainResidue
ESER859
EGLN934
ELYS937
EGLY942
EGLN943
EARG957
ETHR1030
EGLY1031
EFMN2474

site_idCC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE F3S E 2476
ChainResidue
ECYS1102
EILE1103
EMET1104
EVAL1105
EARG1106
EGLN1107
ECYS1108
ECYS1113
EVAL1117
ECYS1118

site_idCC3
Number of Residues10
DetailsBINDING SITE FOR RESIDUE OMT F 2473
ChainResidue
FCYS1
FGLN209
FARG210
FTYR211
FGLN223
FASN231
FGLY232
FGLU233
FASP273
FSER274

site_idCC4
Number of Residues18
DetailsBINDING SITE FOR RESIDUE FMN F 2474
ChainResidue
FPRO856
FGLY857
FMET858
FSER859
FGLU886
FGLN909
FLYS931
FLYS999
FGLY1028
FGLY1029
FTHR1030
FGLY1031
FASP1070
FGLY1071
FGLY1072
FGLY1093
FTHR1094
FAKG2475

site_idCC5
Number of Residues10
DetailsBINDING SITE FOR RESIDUE AKG F 2475
ChainResidue
FSER859
FGLN934
FLYS937
FGLY942
FGLN943
FARG957
FTHR1030
FGLY1031
FALA1032
FFMN2474

site_idCC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE F3S F 2476
ChainResidue
FCYS1102
FILE1103
FMET1104
FVAL1105
FARG1106
FGLN1107
FCYS1108
FCYS1113
FVAL1117
FCYS1118

site_idCC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 G 482
ChainResidue
GCYS59
GILE65
GASN88
GCYS98
GGLN100
GLEU103
GCYS104
GGLU124

site_idCC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 G 483
ChainResidue
GCYS47
GSER48
GCYS50
GCYS55
GCYS108
GVAL109
GILE110
GVAL118
GILE120

site_idCC9
Number of Residues28
DetailsBINDING SITE FOR RESIDUE FAD G 484
ChainResidue
GILE97
GILE153
GGLY154
GGLY156
GPRO157
GALA158
GASP177
GARG178
GTYR179
GGLY184
GLEU185
GLYS194
GGLU219
GVAL220
GALA239
GTHR240
GGLY241
GLEU265
GASP299
GTHR300
GASP303
GASN408
GGLY441
GASP442
GSER448
GLEU449
GVAL450
GALA453

site_idDC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 H 482
ChainResidue
HCYS59
HILE65
HASN88
HCYS98
HGLN100
HLEU103
HCYS104
HGLU124

site_idDC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 H 483
ChainResidue
HCYS47
HSER48
HCYS50
HCYS55
HCYS108
HVAL109
HILE110
HVAL118
HILE120

site_idDC3
Number of Residues28
DetailsBINDING SITE FOR RESIDUE FAD H 484
ChainResidue
HILE97
HILE153
HGLY154
HGLY156
HPRO157
HALA158
HASP177
HARG178
HTYR179
HGLY184
HLEU185
HLYS194
HGLU219
HVAL220
HALA239
HTHR240
HGLY241
HLEU265
HASP299
HTHR300
HASP303
HASN408
HGLY441
HASP442
HSER448
HLEU449
HVAL450
HALA453

site_idDC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 I 482
ChainResidue
ICYS59
IILE65
IASN88
ICYS98
IGLN100
ILEU103
ICYS104
IGLU124

site_idDC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 I 483
ChainResidue
ICYS47
ISER48
ICYS50
ICYS55
ICYS108
IVAL109
IILE110
IVAL118
IILE120

site_idDC6
Number of Residues28
DetailsBINDING SITE FOR RESIDUE FAD I 484
ChainResidue
IILE97
IILE153
IGLY154
IGLY156
IPRO157
IALA158
IASP177
IARG178
ITYR179
IGLY184
ILEU185
ILYS194
IGLU219
IVAL220
IALA239
ITHR240
IGLY241
ILEU265
IASP299
ITHR300
IASP303
IASN408
IGLY441
IASP442
ISER448
ILEU449
IVAL450
IALA453

site_idDC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 J 482
ChainResidue
JCYS59
JILE65
JASN88
JCYS98
JGLN100
JLEU103
JCYS104
JGLU124

site_idDC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 J 483
ChainResidue
JCYS47
JSER48
JCYS50
JCYS55
JCYS108
JVAL109
JILE110
JVAL118
JILE120

site_idDC9
Number of Residues28
DetailsBINDING SITE FOR RESIDUE FAD J 484
ChainResidue
JILE97
JILE153
JGLY154
JGLY156
JPRO157
JALA158
JASP177
JARG178
JTYR179
JGLY184
JLEU185
JLYS194
JGLU219
JVAL220
JALA239
JTHR240
JGLY241
JLEU265
JASP299
JTHR300
JASP303
JASN408
JGLY441
JASP442
JSER448
JLEU449
JVAL450
JALA453

site_idEC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 K 482
ChainResidue
KCYS59
KILE65
KASN88
KCYS98
KGLN100
KLEU103
KCYS104
KGLU124

site_idEC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 K 483
ChainResidue
KCYS47
KSER48
KCYS50
KCYS55
KCYS108
KVAL109
KILE110
KVAL118
KILE120

site_idEC3
Number of Residues28
DetailsBINDING SITE FOR RESIDUE FAD K 484
ChainResidue
KILE97
KILE153
KGLY154
KGLY156
KPRO157
KALA158
KASP177
KARG178
KTYR179
KGLY184
KLEU185
KLYS194
KGLU219
KVAL220
KALA239
KTHR240
KGLY241
KLEU265
KASP299
KTHR300
KASP303
KASN408
KGLY441
KASP442
KSER448
KLEU449
KVAL450
KALA453

site_idEC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SF4 L 482
ChainResidue
LCYS59
LILE65
LASN88
LCYS98
LGLN100
LLEU103
LCYS104
LGLU124

site_idEC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 L 483
ChainResidue
LCYS47
LSER48
LCYS50
LCYS55
LCYS108
LVAL109
LILE110
LVAL118
LILE120

site_idEC6
Number of Residues28
DetailsBINDING SITE FOR RESIDUE FAD L 484
ChainResidue
LILE97
LILE153
LGLY154
LGLY156
LPRO157
LALA158
LASP177
LARG178
LTYR179
LGLY184
LLEU185
LLYS194
LGLU219
LVAL220
LALA239
LTHR240
LGLY241
LLEU265
LASP299
LTHR300
LASP303
LASN408
LGLY441
LASP442
LSER448
LLEU449
LVAL450
LALA453

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues24
DetailsBINDING: BINDING => ECO:0000255
ChainResidueDetails
GCYS94
ICYS98
ICYS104
ICYS108
JCYS94
JCYS98
JCYS104
JCYS108
KCYS94
KCYS98
KCYS104
GCYS98
KCYS108
LCYS94
LCYS98
LCYS104
LCYS108
GCYS104
GCYS108
HCYS94
HCYS98
HCYS104
HCYS108
ICYS94

site_idSWS_FT_FI2
Number of Residues30
DetailsBINDING: BINDING => ECO:0000250
ChainResidueDetails
ALEU1049
BCYS1113
CLEU1049
CSER1050
CCYS1102
CCYS1108
CCYS1113
DLEU1049
DSER1050
DCYS1102
DCYS1108
ASER1050
DCYS1113
ELEU1049
ESER1050
ECYS1102
ECYS1108
ECYS1113
FLEU1049
FSER1050
FCYS1102
FCYS1108
ACYS1102
FCYS1113
ACYS1108
ACYS1113
BLEU1049
BSER1050
BCYS1102
BCYS1108

Catalytic Information from CSA
site_idCSA1
Number of Residues3
DetailsAnnotated By Reference To The Literature 1ofd
ChainResidueDetails
ALYS937
AGLU886
ACYS1

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1ofd
ChainResidueDetails
BLYS937
BGLU886
BCYS1

site_idCSA3
Number of Residues3
DetailsAnnotated By Reference To The Literature 1ofd
ChainResidueDetails
CLYS937
CGLU886
CCYS1

site_idCSA4
Number of Residues3
DetailsAnnotated By Reference To The Literature 1ofd
ChainResidueDetails
DLYS937
DGLU886
DCYS1

site_idCSA5
Number of Residues3
DetailsAnnotated By Reference To The Literature 1ofd
ChainResidueDetails
ELYS937
EGLU886
ECYS1

site_idCSA6
Number of Residues3
DetailsAnnotated By Reference To The Literature 1ofd
ChainResidueDetails
FLYS937
FGLU886
FCYS1

site_idMCSA1
Number of Residues6
DetailsM-CSA 304
ChainResidueDetails
ACYS1covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
AASN231electrostatic stabiliser, hydrogen bond donor
AGLY232electrostatic stabiliser, hydrogen bond donor
AMET479single electron acceptor, single electron donor, single electron relay
AGLU886proton acceptor, proton donor, proton relay
ALYS937electrostatic stabiliser

site_idMCSA2
Number of Residues6
DetailsM-CSA 304
ChainResidueDetails
BCYS1covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
BASN231electrostatic stabiliser, hydrogen bond donor
BGLY232electrostatic stabiliser, hydrogen bond donor
BMET479single electron acceptor, single electron donor, single electron relay
BGLU886proton acceptor, proton donor, proton relay
BLYS937electrostatic stabiliser

site_idMCSA3
Number of Residues6
DetailsM-CSA 304
ChainResidueDetails
CCYS1covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
CASN231electrostatic stabiliser, hydrogen bond donor
CGLY232electrostatic stabiliser, hydrogen bond donor
CMET479single electron acceptor, single electron donor, single electron relay
CGLU886proton acceptor, proton donor, proton relay
CLYS937electrostatic stabiliser

site_idMCSA4
Number of Residues6
DetailsM-CSA 304
ChainResidueDetails
DCYS1covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
DASN231electrostatic stabiliser, hydrogen bond donor
DGLY232electrostatic stabiliser, hydrogen bond donor
DMET479single electron acceptor, single electron donor, single electron relay
DGLU886proton acceptor, proton donor, proton relay
DLYS937electrostatic stabiliser

site_idMCSA5
Number of Residues6
DetailsM-CSA 304
ChainResidueDetails
ECYS1covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
EASN231electrostatic stabiliser, hydrogen bond donor
EGLY232electrostatic stabiliser, hydrogen bond donor
EMET479single electron acceptor, single electron donor, single electron relay
EGLU886proton acceptor, proton donor, proton relay
ELYS937electrostatic stabiliser

site_idMCSA6
Number of Residues6
DetailsM-CSA 304
ChainResidueDetails
FCYS1covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
FASN231electrostatic stabiliser, hydrogen bond donor
FGLY232electrostatic stabiliser, hydrogen bond donor
FMET479single electron acceptor, single electron donor, single electron relay
FGLU886proton acceptor, proton donor, proton relay
FLYS937electrostatic stabiliser

225158

PDB entries from 2024-09-18

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