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6LGM

Crystal structure of an oxido-reductase with mutation and inhibitor

Functional Information from GO Data
ChainGOidnamespacecontents
A0000226biological_processmicrotubule cytoskeleton organization
A0004365molecular_functionglyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005829cellular_componentcytosol
A0005856cellular_componentcytoskeleton
A0005886cellular_componentplasma membrane
A0006006biological_processglucose metabolic process
A0006094biological_processgluconeogenesis
A0006096biological_processglycolytic process
A0006417biological_processregulation of translation
A0006915biological_processapoptotic process
A0008017molecular_functionmicrotubule binding
A0015630cellular_componentmicrotubule cytoskeleton
A0016491molecular_functionoxidoreductase activity
A0016620molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
A0016740molecular_functiontransferase activity
A0017148biological_processnegative regulation of translation
A0019899molecular_functionenzyme binding
A0031906cellular_componentlate endosome lumen
A0032481biological_processpositive regulation of type I interferon production
A0035605molecular_functionpeptidyl-cysteine S-nitrosylase activity
A0035606biological_processpeptidyl-cysteine S-trans-nitrosylation
A0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
A0043209cellular_componentmyelin sheath
A0045087biological_processinnate immune response
A0046166biological_processglyceraldehyde-3-phosphate biosynthetic process
A0050661molecular_functionNADP binding
A0050821biological_processprotein stabilization
A0051287molecular_functionNAD binding
A0051402biological_processneuron apoptotic process
A0061621biological_processcanonical glycolysis
A0097452cellular_componentGAIT complex
B0000226biological_processmicrotubule cytoskeleton organization
B0004365molecular_functionglyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005829cellular_componentcytosol
B0005856cellular_componentcytoskeleton
B0005886cellular_componentplasma membrane
B0006006biological_processglucose metabolic process
B0006094biological_processgluconeogenesis
B0006096biological_processglycolytic process
B0006417biological_processregulation of translation
B0006915biological_processapoptotic process
B0008017molecular_functionmicrotubule binding
B0015630cellular_componentmicrotubule cytoskeleton
B0016491molecular_functionoxidoreductase activity
B0016620molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
B0016740molecular_functiontransferase activity
B0017148biological_processnegative regulation of translation
B0019899molecular_functionenzyme binding
B0031906cellular_componentlate endosome lumen
B0032481biological_processpositive regulation of type I interferon production
B0035605molecular_functionpeptidyl-cysteine S-nitrosylase activity
B0035606biological_processpeptidyl-cysteine S-trans-nitrosylation
B0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
B0043209cellular_componentmyelin sheath
B0045087biological_processinnate immune response
B0046166biological_processglyceraldehyde-3-phosphate biosynthetic process
B0050661molecular_functionNADP binding
B0050821biological_processprotein stabilization
B0051287molecular_functionNAD binding
B0051402biological_processneuron apoptotic process
B0061621biological_processcanonical glycolysis
B0097452cellular_componentGAIT complex
C0000226biological_processmicrotubule cytoskeleton organization
C0004365molecular_functionglyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005739cellular_componentmitochondrion
C0005829cellular_componentcytosol
C0005856cellular_componentcytoskeleton
C0005886cellular_componentplasma membrane
C0006006biological_processglucose metabolic process
C0006094biological_processgluconeogenesis
C0006096biological_processglycolytic process
C0006417biological_processregulation of translation
C0006915biological_processapoptotic process
C0008017molecular_functionmicrotubule binding
C0015630cellular_componentmicrotubule cytoskeleton
C0016491molecular_functionoxidoreductase activity
C0016620molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
C0016740molecular_functiontransferase activity
C0017148biological_processnegative regulation of translation
C0019899molecular_functionenzyme binding
C0031906cellular_componentlate endosome lumen
C0032481biological_processpositive regulation of type I interferon production
C0035605molecular_functionpeptidyl-cysteine S-nitrosylase activity
C0035606biological_processpeptidyl-cysteine S-trans-nitrosylation
C0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
C0043209cellular_componentmyelin sheath
C0045087biological_processinnate immune response
C0046166biological_processglyceraldehyde-3-phosphate biosynthetic process
C0050661molecular_functionNADP binding
C0050821biological_processprotein stabilization
C0051287molecular_functionNAD binding
C0051402biological_processneuron apoptotic process
C0061621biological_processcanonical glycolysis
C0097452cellular_componentGAIT complex
D0000226biological_processmicrotubule cytoskeleton organization
D0004365molecular_functionglyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005739cellular_componentmitochondrion
D0005829cellular_componentcytosol
D0005856cellular_componentcytoskeleton
D0005886cellular_componentplasma membrane
D0006006biological_processglucose metabolic process
D0006094biological_processgluconeogenesis
D0006096biological_processglycolytic process
D0006417biological_processregulation of translation
D0006915biological_processapoptotic process
D0008017molecular_functionmicrotubule binding
D0015630cellular_componentmicrotubule cytoskeleton
D0016491molecular_functionoxidoreductase activity
D0016620molecular_functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
D0016740molecular_functiontransferase activity
D0017148biological_processnegative regulation of translation
D0019899molecular_functionenzyme binding
D0031906cellular_componentlate endosome lumen
D0032481biological_processpositive regulation of type I interferon production
D0035605molecular_functionpeptidyl-cysteine S-nitrosylase activity
D0035606biological_processpeptidyl-cysteine S-trans-nitrosylation
D0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
D0043209cellular_componentmyelin sheath
D0045087biological_processinnate immune response
D0046166biological_processglyceraldehyde-3-phosphate biosynthetic process
D0050661molecular_functionNADP binding
D0050821biological_processprotein stabilization
D0051287molecular_functionNAD binding
D0051402biological_processneuron apoptotic process
D0061621biological_processcanonical glycolysis
D0097452cellular_componentGAIT complex
Functional Information from PDB Data
site_idAC1
Number of Residues30
Detailsbinding site for residue NAD A 401
ChainResidue
AASN9
AARG80
ASER98
ATHR99
AGLY100
APHE102
ASER122
AALA123
AALA183
AASN316
ATYR320
AGLY10
APO4402
A9HB403
AHOH514
AHOH519
AHOH522
AHOH523
AHOH534
AHOH537
AHOH576
AHOH594
AGLY12
CPRO191
AARG13
AILE14
AASN34
AASP35
APRO36
APHE37

site_idAC2
Number of Residues5
Detailsbinding site for residue PO4 A 402
ChainResidue
ATHR182
ATHR184
AARG234
ANAD401
AHOH531

site_idAC3
Number of Residues9
Detailsbinding site for residue 9HB A 403
ChainResidue
APRO124
ASER151
ASER152
ATHR153
ATHR211
AGLY212
AALA213
ANAD401
AHOH537

site_idAC4
Number of Residues26
Detailsbinding site for residue NAD B 401
ChainResidue
BASN9
BGLY10
BPHE11
BGLY12
BARG13
BILE14
BASN34
BASP35
BPRO36
BPHE37
BARG80
BSER98
BTHR99
BGLY100
BPHE102
BSER122
BALA123
BSER152
BALA183
BASN316
BTYR320
BPO4402
B9HB403
BHOH528
BHOH564
DPRO191

site_idAC5
Number of Residues5
Detailsbinding site for residue PO4 B 402
ChainResidue
BTHR182
BARG234
BNAD401
B9HB403
BHOH501

site_idAC6
Number of Residues9
Detailsbinding site for residue 9HB B 403
ChainResidue
BSER151
BSER152
BTHR153
BHIS179
BTHR211
BGLY212
BALA213
BNAD401
BPO4402

site_idAC7
Number of Residues27
Detailsbinding site for residue NAD C 401
ChainResidue
CSER122
CALA123
CALA183
CASN316
CTYR320
CPO4402
C9HB403
CHOH526
CHOH541
CHOH544
CHOH559
CHOH560
APRO191
CASN9
CGLY10
CGLY12
CARG13
CILE14
CASN34
CASP35
CPRO36
CPHE37
CARG80
CSER98
CTHR99
CGLY100
CPHE102

site_idAC8
Number of Residues5
Detailsbinding site for residue PO4 C 402
ChainResidue
CTHR182
CTHR184
CARG234
CNAD401
C9HB403

site_idAC9
Number of Residues9
Detailsbinding site for residue 9HB C 403
ChainResidue
CSER151
CSER152
CTHR153
CHIS179
CTHR211
CGLY212
CALA213
CNAD401
CPO4402

site_idAD1
Number of Residues6
Detailsbinding site for residue PO4 D 401
ChainResidue
DSER151
DTHR211
DGLY212
DALA213
DHOH510
DHOH573

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE: Nucleophile => ECO:0000255|PROSITE-ProRule:PRU10009
ChainResidueDetails
ASER152
BSER152
CSER152
DSER152

site_idSWS_FT_FI2
Number of Residues20
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
AARG13
BASN316
CARG13
CASP35
CARG80
CSER122
CASN316
DARG13
DASP35
DARG80
DSER122
AASP35
DASN316
AARG80
ASER122
AASN316
BARG13
BASP35
BARG80
BSER122

site_idSWS_FT_FI3
Number of Residues16
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P22513
ChainResidueDetails
ASER151
CTHR182
CTHR211
CARG234
DSER151
DTHR182
DTHR211
DARG234
ATHR182
ATHR211
AARG234
BSER151
BTHR182
BTHR211
BARG234
CSER151

site_idSWS_FT_FI4
Number of Residues4
DetailsSITE: Activates thiol group during catalysis => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
AHIS179
BHIS179
CHIS179
DHIS179

site_idSWS_FT_FI5
Number of Residues20
DetailsMOD_RES: N6,N6-dimethyllysine => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ALYS5
BLYS334
CLYS5
CLYS66
CLYS260
CLYS263
CLYS334
DLYS5
DLYS66
DLYS260
DLYS263
ALYS66
DLYS334
ALYS260
ALYS263
ALYS334
BLYS5
BLYS66
BLYS260
BLYS263

site_idSWS_FT_FI6
Number of Residues28
DetailsMOD_RES: Deamidated asparagine => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
AASN9
BASN70
BASN149
BASN155
BASN225
BASN316
CASN9
CASN64
CASN70
CASN149
CASN155
AASN64
CASN225
CASN316
DASN9
DASN64
DASN70
DASN149
DASN155
DASN225
DASN316
AASN70
AASN149
AASN155
AASN225
AASN316
BASN9
BASN64

site_idSWS_FT_FI7
Number of Residues4
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ATYR42
BTYR42
CTYR42
DTYR42

site_idSWS_FT_FI8
Number of Residues12
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ALYS61
DLYS61
DLYS219
DLYS254
ALYS219
ALYS254
BLYS61
BLYS219
BLYS254
CLYS61
CLYS219
CLYS254

site_idSWS_FT_FI9
Number of Residues32
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ATHR75
BTHR153
BTHR177
BTHR182
BTHR184
BTHR211
BTHR229
BTHR237
CTHR75
CTHR153
CTHR177
ATHR153
CTHR182
CTHR184
CTHR211
CTHR229
CTHR237
DTHR75
DTHR153
DTHR177
DTHR182
DTHR184
ATHR177
DTHR211
DTHR229
DTHR237
ATHR182
ATHR184
ATHR211
ATHR229
ATHR237
BTHR75

site_idSWS_FT_FI10
Number of Residues24
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ASER122
BSER241
BSER312
BSER333
CSER122
CSER148
CSER151
CSER241
CSER312
CSER333
DSER122
ASER148
DSER148
DSER151
DSER241
DSER312
DSER333
ASER151
ASER241
ASER312
ASER333
BSER122
BSER148
BSER151

site_idSWS_FT_FI11
Number of Residues4
DetailsMOD_RES: S-nitrosocysteine; in reversibly inhibited form => ECO:0000250|UniProtKB:P04797
ChainResidueDetails
ASER152
BSER152
CSER152
DSER152

site_idSWS_FT_FI12
Number of Residues8
DetailsMOD_RES: N6-malonyllysine; alternate => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ALYS194
ALYS215
BLYS194
BLYS215
CLYS194
CLYS215
DLYS194
DLYS215

site_idSWS_FT_FI13
Number of Residues4
DetailsMOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ALYS227
BLYS227
CLYS227
DLYS227

site_idSWS_FT_FI14
Number of Residues4
DetailsMOD_RES: S-nitrosocysteine => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ACYS247
BCYS247
CCYS247
DCYS247

site_idSWS_FT_FI15
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0000250|UniProtKB:P04406
ChainResidueDetails
ALYS186
BLYS186
CLYS186
DLYS186

227344

PDB entries from 2024-11-13

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