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3JD4

Glutamate dehydrogenase in complex with NADH and GTP, closed conformation

Functional Information from GO Data
ChainGOidnamespacecontents
A0004352molecular_functionglutamate dehydrogenase (NAD+) activity
A0004353molecular_functionglutamate dehydrogenase [NAD(P)+] activity
A0004354molecular_functionglutamate dehydrogenase (NADP+) activity
A0005524molecular_functionATP binding
A0005525molecular_functionGTP binding
A0005739cellular_componentmitochondrion
A0005743cellular_componentmitochondrial inner membrane
A0005783cellular_componentendoplasmic reticulum
A0006520biological_processamino acid metabolic process
A0006538biological_processglutamate catabolic process
A0006541biological_processglutamine metabolic process
A0016491molecular_functionoxidoreductase activity
A0016639molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
A0042802molecular_functionidentical protein binding
A0072350biological_processtricarboxylic acid metabolic process
B0004352molecular_functionglutamate dehydrogenase (NAD+) activity
B0004353molecular_functionglutamate dehydrogenase [NAD(P)+] activity
B0004354molecular_functionglutamate dehydrogenase (NADP+) activity
B0005524molecular_functionATP binding
B0005525molecular_functionGTP binding
B0005739cellular_componentmitochondrion
B0005743cellular_componentmitochondrial inner membrane
B0005783cellular_componentendoplasmic reticulum
B0006520biological_processamino acid metabolic process
B0006538biological_processglutamate catabolic process
B0006541biological_processglutamine metabolic process
B0016491molecular_functionoxidoreductase activity
B0016639molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
B0042802molecular_functionidentical protein binding
B0072350biological_processtricarboxylic acid metabolic process
C0004352molecular_functionglutamate dehydrogenase (NAD+) activity
C0004353molecular_functionglutamate dehydrogenase [NAD(P)+] activity
C0004354molecular_functionglutamate dehydrogenase (NADP+) activity
C0005524molecular_functionATP binding
C0005525molecular_functionGTP binding
C0005739cellular_componentmitochondrion
C0005743cellular_componentmitochondrial inner membrane
C0005783cellular_componentendoplasmic reticulum
C0006520biological_processamino acid metabolic process
C0006538biological_processglutamate catabolic process
C0006541biological_processglutamine metabolic process
C0016491molecular_functionoxidoreductase activity
C0016639molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
C0042802molecular_functionidentical protein binding
C0072350biological_processtricarboxylic acid metabolic process
D0004352molecular_functionglutamate dehydrogenase (NAD+) activity
D0004353molecular_functionglutamate dehydrogenase [NAD(P)+] activity
D0004354molecular_functionglutamate dehydrogenase (NADP+) activity
D0005524molecular_functionATP binding
D0005525molecular_functionGTP binding
D0005739cellular_componentmitochondrion
D0005743cellular_componentmitochondrial inner membrane
D0005783cellular_componentendoplasmic reticulum
D0006520biological_processamino acid metabolic process
D0006538biological_processglutamate catabolic process
D0006541biological_processglutamine metabolic process
D0016491molecular_functionoxidoreductase activity
D0016639molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
D0042802molecular_functionidentical protein binding
D0072350biological_processtricarboxylic acid metabolic process
E0004352molecular_functionglutamate dehydrogenase (NAD+) activity
E0004353molecular_functionglutamate dehydrogenase [NAD(P)+] activity
E0004354molecular_functionglutamate dehydrogenase (NADP+) activity
E0005524molecular_functionATP binding
E0005525molecular_functionGTP binding
E0005739cellular_componentmitochondrion
E0005743cellular_componentmitochondrial inner membrane
E0005783cellular_componentendoplasmic reticulum
E0006520biological_processamino acid metabolic process
E0006538biological_processglutamate catabolic process
E0006541biological_processglutamine metabolic process
E0016491molecular_functionoxidoreductase activity
E0016639molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
E0042802molecular_functionidentical protein binding
E0072350biological_processtricarboxylic acid metabolic process
F0004352molecular_functionglutamate dehydrogenase (NAD+) activity
F0004353molecular_functionglutamate dehydrogenase [NAD(P)+] activity
F0004354molecular_functionglutamate dehydrogenase (NADP+) activity
F0005524molecular_functionATP binding
F0005525molecular_functionGTP binding
F0005739cellular_componentmitochondrion
F0005743cellular_componentmitochondrial inner membrane
F0005783cellular_componentendoplasmic reticulum
F0006520biological_processamino acid metabolic process
F0006538biological_processglutamate catabolic process
F0006541biological_processglutamine metabolic process
F0016491molecular_functionoxidoreductase activity
F0016639molecular_functionoxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
F0042802molecular_functionidentical protein binding
F0072350biological_processtricarboxylic acid metabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues16
DetailsBINDING SITE FOR RESIDUE NAI A 601
ChainResidue
AARG94
AVAL255
AGLU275
ASER276
AALA325
AALA326
AGLY347
AASN349
AASP168
AMET169
ASER170
ATHR215
AGLN250
AGLY251
AGLY253
AASN254

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GTP A 602
ChainResidue
AHIS209
ASER213
AARG261
ATYR262
AARG265
AGLU292
AHIS450

site_idAC3
Number of Residues17
DetailsBINDING SITE FOR RESIDUE NAI A 603
ChainResidue
AHIS195
AGLN205
AGLY206
AASN387
AASN388
AHIS391
AVAL392
ASER393
AGLU445
CHIS85
CARG86
CTHR87
CCYS115
CASP119
CVAL120
CPRO121
CLYS488

site_idAC4
Number of Residues17
DetailsBINDING SITE FOR RESIDUE NAI B 601
ChainResidue
AHIS85
AARG86
ATHR87
ACYS115
AASP119
AVAL120
APRO121
ALYS488
BHIS195
BGLN205
BGLY206
BASN387
BASN388
BHIS391
BVAL392
BSER393
BGLU445

site_idAC5
Number of Residues16
DetailsBINDING SITE FOR RESIDUE NAI B 602
ChainResidue
BARG94
BASP168
BMET169
BSER170
BTHR215
BGLN250
BGLY251
BGLY253
BASN254
BVAL255
BGLU275
BSER276
BALA325
BALA326
BGLY347
BASN349

site_idAC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GTP B 603
ChainResidue
BHIS209
BSER213
BARG261
BTYR262
BARG265
BGLU292
BHIS450

site_idAC7
Number of Residues17
DetailsBINDING SITE FOR RESIDUE NAI C 601
ChainResidue
BHIS85
BARG86
BTHR87
BCYS115
BASP119
BVAL120
BPRO121
BLYS488
CHIS195
CGLN205
CGLY206
CASN387
CASN388
CHIS391
CVAL392
CSER393
CGLU445

site_idAC8
Number of Residues17
DetailsBINDING SITE FOR RESIDUE NAI C 602
ChainResidue
CMET169
CSER170
CTHR215
CGLN250
CGLY251
CGLY253
CASN254
CVAL255
CGLU275
CSER276
CALA325
CALA326
CGLY347
CASN349
CASN374
CARG94
CASP168

site_idAC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GTP C 603
ChainResidue
CHIS209
CSER213
CARG261
CTYR262
CARG265
CGLU292
CHIS450

site_idBC1
Number of Residues16
DetailsBINDING SITE FOR RESIDUE NAI D 601
ChainResidue
DARG94
DASP168
DMET169
DSER170
DTHR215
DGLN250
DGLY251
DGLY253
DASN254
DVAL255
DGLU275
DSER276
DALA325
DALA326
DGLY347
DASN349

site_idBC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GTP D 602
ChainResidue
DHIS209
DSER213
DARG261
DTYR262
DARG265
DGLU292
DHIS450

site_idBC3
Number of Residues17
DetailsBINDING SITE FOR RESIDUE NAI D 603
ChainResidue
DHIS195
DGLN205
DGLY206
DASN387
DASN388
DHIS391
DVAL392
DSER393
DGLU445
FHIS85
FARG86
FTHR87
FCYS115
FASP119
FVAL120
FPRO121
FLYS488

site_idBC4
Number of Residues17
DetailsBINDING SITE FOR RESIDUE NAI E 601
ChainResidue
DHIS85
DARG86
DTHR87
DCYS115
DASP119
DVAL120
DPRO121
DLYS488
EHIS195
EGLN205
EGLY206
EASN387
EASN388
EHIS391
EVAL392
ESER393
EGLU445

site_idBC5
Number of Residues16
DetailsBINDING SITE FOR RESIDUE NAI E 602
ChainResidue
EARG94
EASP168
EMET169
ESER170
ETHR215
EGLN250
EGLY251
EGLY253
EASN254
EVAL255
EGLU275
ESER276
EALA325
EALA326
EGLY347
EASN349

site_idBC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GTP E 603
ChainResidue
EHIS209
ESER213
EARG261
ETYR262
EARG265
EGLU292
EHIS450

site_idBC7
Number of Residues17
DetailsBINDING SITE FOR RESIDUE NAI F 601
ChainResidue
EHIS85
EARG86
ETHR87
ECYS115
EASP119
EVAL120
EPRO121
ELYS488
FHIS195
FGLN205
FGLY206
FASN387
FASN388
FHIS391
FVAL392
FSER393
FGLU445

site_idBC8
Number of Residues17
DetailsBINDING SITE FOR RESIDUE NAI F 602
ChainResidue
FARG94
FASP168
FMET169
FSER170
FTHR215
FGLN250
FGLY251
FGLY253
FASN254
FVAL255
FGLU275
FSER276
FALA325
FALA326
FGLY347
FASN349
FASN374

site_idBC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GTP F 603
ChainResidue
FHIS209
FSER213
FARG261
FTYR262
FARG265
FGLU292
FHIS450

Functional Information from PROSITE/UniProt
site_idPS00074
Number of Residues14
DetailsGLFV_DEHYDROGENASE Glu / Leu / Phe / Val dehydrogenases active site. VpfGGAKaGvkiNP
ChainResidueDetails
AVAL120-PRO133

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
DetailsACT_SITE: ACT_SITE => ECO:0000255|PROSITE-ProRule:PRU10011
ChainResidueDetails
ALYS126
BLYS126
CLYS126
DLYS126
ELYS126
FLYS126

site_idSWS_FT_FI2
Number of Residues66
DetailsBINDING: BINDING => ECO:0000269|PubMed:11254391
ChainResidueDetails
AGLN84
ASER381
AASN387
BGLN84
BLYS90
BLYS114
BASP119
BHIS195
BHIS209
BSER213
BTYR262
ALYS90
BARG265
BSER381
BASN387
CGLN84
CLYS90
CLYS114
CASP119
CHIS195
CHIS209
CSER213
ALYS114
CTYR262
CARG265
CSER381
CASN387
DGLN84
DLYS90
DLYS114
DASP119
DHIS195
DHIS209
AASP119
DSER213
DTYR262
DARG265
DSER381
DASN387
EGLN84
ELYS90
ELYS114
EASP119
EHIS195
AHIS195
EHIS209
ESER213
ETYR262
EARG265
ESER381
EASN387
FGLN84
FLYS90
FLYS114
FASP119
AHIS209
FHIS195
FHIS209
FSER213
FTYR262
FARG265
FSER381
FASN387
ASER213
ATYR262
AARG265

site_idSWS_FT_FI3
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:12653548
ChainResidueDetails
ASER393
EARG459
FSER393
FARG459
AARG459
BSER393
BARG459
CSER393
CARG459
DSER393
DARG459
ESER393

site_idSWS_FT_FI4
Number of Residues12
DetailsMOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P26443
ChainResidueDetails
ALYS11
ELYS143
FLYS11
FLYS143
ALYS143
BLYS11
BLYS143
CLYS11
CLYS143
DLYS11
DLYS143
ELYS11

site_idSWS_FT_FI5
Number of Residues12
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P26443
ChainResidueDetails
ASER22
ESER71
FSER22
FSER71
ASER71
BSER22
BSER71
CSER22
CSER71
DSER22
DSER71
ESER22

site_idSWS_FT_FI6
Number of Residues54
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22076378
ChainResidueDetails
ALYS27
BLYS27
BLYS53
BLYS105
BLYS306
BLYS358
BLYS400
BLYS446
BLYS470
BLYS488
CLYS27
ALYS53
CLYS53
CLYS105
CLYS306
CLYS358
CLYS400
CLYS446
CLYS470
CLYS488
DLYS27
DLYS53
ALYS105
DLYS105
DLYS306
DLYS358
DLYS400
DLYS446
DLYS470
DLYS488
ELYS27
ELYS53
ELYS105
ALYS306
ELYS306
ELYS358
ELYS400
ELYS446
ELYS470
ELYS488
FLYS27
FLYS53
FLYS105
FLYS306
ALYS358
FLYS358
FLYS400
FLYS446
FLYS470
FLYS488
ALYS400
ALYS446
ALYS470
ALYS488

site_idSWS_FT_FI7
Number of Residues18
DetailsMOD_RES: N6-acetyllysine => ECO:0000269|PubMed:22076378
ChainResidueDetails
ALYS33
DLYS33
DLYS329
DLYS342
ELYS33
ELYS329
ELYS342
FLYS33
FLYS329
FLYS342
ALYS329
ALYS342
BLYS33
BLYS329
BLYS342
CLYS33
CLYS329
CLYS342

site_idSWS_FT_FI8
Number of Residues6
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P26443
ChainResidueDetails
ATYR78
BTYR78
CTYR78
DTYR78
ETYR78
FTYR78

site_idSWS_FT_FI9
Number of Residues6
DetailsMOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P00367
ChainResidueDetails
ALYS90
BLYS90
CLYS90
DLYS90
ELYS90
FLYS90

site_idSWS_FT_FI10
Number of Residues24
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P26443
ChainResidueDetails
ALYS114
CLYS130
CLYS154
CLYS269
DLYS114
DLYS130
DLYS154
DLYS269
ELYS114
ELYS130
ELYS154
ALYS130
ELYS269
FLYS114
FLYS130
FLYS154
FLYS269
ALYS154
ALYS269
BLYS114
BLYS130
BLYS154
BLYS269
CLYS114

site_idSWS_FT_FI11
Number of Residues6
DetailsMOD_RES: ADP-ribosylcysteine => ECO:0000250|UniProtKB:P00367
ChainResidueDetails
ACYS115
BCYS115
CCYS115
DCYS115
ECYS115
FCYS115

site_idSWS_FT_FI12
Number of Residues48
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P26443
ChainResidueDetails
ALYS126
BLYS134
BLYS289
BLYS295
BLYS308
BLYS333
BLYS420
BLYS423
CLYS126
CLYS134
CLYS289
ALYS134
CLYS295
CLYS308
CLYS333
CLYS420
CLYS423
DLYS126
DLYS134
DLYS289
DLYS295
DLYS308
ALYS289
DLYS333
DLYS420
DLYS423
ELYS126
ELYS134
ELYS289
ELYS295
ELYS308
ELYS333
ELYS420
ALYS295
ELYS423
FLYS126
FLYS134
FLYS289
FLYS295
FLYS308
FLYS333
FLYS420
FLYS423
ALYS308
ALYS333
ALYS420
ALYS423
BLYS126

site_idSWS_FT_FI13
Number of Residues12
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P00367
ChainResidueDetails
ASER170
ESER327
FSER170
FSER327
ASER327
BSER170
BSER327
CSER170
CSER327
DSER170
DSER327
ESER170

site_idSWS_FT_FI14
Number of Residues6
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P10860
ChainResidueDetails
ATHR353
BTHR353
CTHR353
DTHR353
ETHR353
FTHR353

site_idSWS_FT_FI15
Number of Residues6
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P00367
ChainResidueDetails
ATYR455
BTYR455
CTYR455
DTYR455
ETYR455
FTYR455

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PDB entries from 2024-08-07

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