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1T0L

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(2+)

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0004450molecular_functionisocitrate dehydrogenase (NADP+) activity
A0005515molecular_functionprotein binding
A0005576cellular_componentextracellular region
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005777cellular_componentperoxisome
A0005782cellular_componentperoxisomal matrix
A0005829cellular_componentcytosol
A0006097biological_processglyoxylate cycle
A0006099biological_processtricarboxylic acid cycle
A0006102biological_processisocitrate metabolic process
A0006103biological_process2-oxoglutarate metabolic process
A0006739biological_processNADP metabolic process
A0006749biological_processglutathione metabolic process
A0006979biological_processresponse to oxidative stress
A0008585biological_processfemale gonad development
A0014070biological_processresponse to organic cyclic compound
A0016491molecular_functionoxidoreductase activity
A0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A0034774cellular_componentsecretory granule lumen
A0042802molecular_functionidentical protein binding
A0042803molecular_functionprotein homodimerization activity
A0045296molecular_functioncadherin binding
A0046872molecular_functionmetal ion binding
A0048545biological_processresponse to steroid hormone
A0050661molecular_functionNADP binding
A0051287molecular_functionNAD binding
A0060696biological_processregulation of phospholipid catabolic process
A0070062cellular_componentextracellular exosome
A0071071biological_processregulation of phospholipid biosynthetic process
A1904724cellular_componenttertiary granule lumen
A1904813cellular_componentficolin-1-rich granule lumen
B0000287molecular_functionmagnesium ion binding
B0004450molecular_functionisocitrate dehydrogenase (NADP+) activity
B0005515molecular_functionprotein binding
B0005576cellular_componentextracellular region
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005777cellular_componentperoxisome
B0005782cellular_componentperoxisomal matrix
B0005829cellular_componentcytosol
B0006097biological_processglyoxylate cycle
B0006099biological_processtricarboxylic acid cycle
B0006102biological_processisocitrate metabolic process
B0006103biological_process2-oxoglutarate metabolic process
B0006739biological_processNADP metabolic process
B0006749biological_processglutathione metabolic process
B0006979biological_processresponse to oxidative stress
B0008585biological_processfemale gonad development
B0014070biological_processresponse to organic cyclic compound
B0016491molecular_functionoxidoreductase activity
B0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B0034774cellular_componentsecretory granule lumen
B0042802molecular_functionidentical protein binding
B0042803molecular_functionprotein homodimerization activity
B0045296molecular_functioncadherin binding
B0046872molecular_functionmetal ion binding
B0048545biological_processresponse to steroid hormone
B0050661molecular_functionNADP binding
B0051287molecular_functionNAD binding
B0060696biological_processregulation of phospholipid catabolic process
B0070062cellular_componentextracellular exosome
B0071071biological_processregulation of phospholipid biosynthetic process
B1904724cellular_componenttertiary granule lumen
B1904813cellular_componentficolin-1-rich granule lumen
C0000287molecular_functionmagnesium ion binding
C0004450molecular_functionisocitrate dehydrogenase (NADP+) activity
C0005515molecular_functionprotein binding
C0005576cellular_componentextracellular region
C0005737cellular_componentcytoplasm
C0005739cellular_componentmitochondrion
C0005777cellular_componentperoxisome
C0005782cellular_componentperoxisomal matrix
C0005829cellular_componentcytosol
C0006097biological_processglyoxylate cycle
C0006099biological_processtricarboxylic acid cycle
C0006102biological_processisocitrate metabolic process
C0006103biological_process2-oxoglutarate metabolic process
C0006739biological_processNADP metabolic process
C0006749biological_processglutathione metabolic process
C0006979biological_processresponse to oxidative stress
C0008585biological_processfemale gonad development
C0014070biological_processresponse to organic cyclic compound
C0016491molecular_functionoxidoreductase activity
C0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C0034774cellular_componentsecretory granule lumen
C0042802molecular_functionidentical protein binding
C0042803molecular_functionprotein homodimerization activity
C0045296molecular_functioncadherin binding
C0046872molecular_functionmetal ion binding
C0048545biological_processresponse to steroid hormone
C0050661molecular_functionNADP binding
C0051287molecular_functionNAD binding
C0060696biological_processregulation of phospholipid catabolic process
C0070062cellular_componentextracellular exosome
C0071071biological_processregulation of phospholipid biosynthetic process
C1904724cellular_componenttertiary granule lumen
C1904813cellular_componentficolin-1-rich granule lumen
D0000287molecular_functionmagnesium ion binding
D0004450molecular_functionisocitrate dehydrogenase (NADP+) activity
D0005515molecular_functionprotein binding
D0005576cellular_componentextracellular region
D0005737cellular_componentcytoplasm
D0005739cellular_componentmitochondrion
D0005777cellular_componentperoxisome
D0005782cellular_componentperoxisomal matrix
D0005829cellular_componentcytosol
D0006097biological_processglyoxylate cycle
D0006099biological_processtricarboxylic acid cycle
D0006102biological_processisocitrate metabolic process
D0006103biological_process2-oxoglutarate metabolic process
D0006739biological_processNADP metabolic process
D0006749biological_processglutathione metabolic process
D0006979biological_processresponse to oxidative stress
D0008585biological_processfemale gonad development
D0014070biological_processresponse to organic cyclic compound
D0016491molecular_functionoxidoreductase activity
D0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D0034774cellular_componentsecretory granule lumen
D0042802molecular_functionidentical protein binding
D0042803molecular_functionprotein homodimerization activity
D0045296molecular_functioncadherin binding
D0046872molecular_functionmetal ion binding
D0048545biological_processresponse to steroid hormone
D0050661molecular_functionNADP binding
D0051287molecular_functionNAD binding
D0060696biological_processregulation of phospholipid catabolic process
D0070062cellular_componentextracellular exosome
D0071071biological_processregulation of phospholipid biosynthetic process
D1904724cellular_componenttertiary granule lumen
D1904813cellular_componentficolin-1-rich granule lumen
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 1717
ChainResidue
AARG109
AASP275
AASP279
AICT1616
AHOH1763
BASP252

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CA B 1718
ChainResidue
BICT1617
BHOH1897
AASP252
BASP275
BASP279

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA C 1719
ChainResidue
CASP275
CASP279
CICT1618
CHOH1733
CHOH1859
DASP252

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA D 1720
ChainResidue
CASP252
DASP275
DASP279
DICT1619
DHOH1806
DHOH1815

site_idAC5
Number of Residues31
DetailsBINDING SITE FOR RESIDUE NAP A 1515
ChainResidue
ALYS72
AALA74
ATHR75
AILE76
ATHR77
AARG82
AASN96
ALEU288
AALA308
AHIS309
AGLY310
ATHR311
AVAL312
ATHR313
AARG314
AHIS315
ATHR327
AASN328
AICT1616
AHOH1718
AHOH1720
AHOH1773
AHOH1782
AHOH1807
AHOH1844
AHOH1856
AHOH1859
AHOH1914
BGLN257
BLYS260
BHOH1799

site_idAC6
Number of Residues29
DetailsBINDING SITE FOR RESIDUE NAP B 1516
ChainResidue
AASP253
AGLN257
ALYS260
BLYS72
BALA74
BTHR75
BILE76
BTHR77
BARG82
BASN96
BLEU288
BALA308
BHIS309
BGLY310
BTHR311
BVAL312
BTHR313
BARG314
BHIS315
BASN328
BICT1617
BHOH1721
BHOH1722
BHOH1737
BHOH1741
BHOH1749
BHOH1803
BHOH1872
BHOH1897

site_idAC7
Number of Residues31
DetailsBINDING SITE FOR RESIDUE NAP C 1517
ChainResidue
CTHR327
CASN328
CICT1618
CHOH1723
CHOH1727
CHOH1739
CHOH1743
CHOH1746
CHOH1793
CHOH1819
CHOH1852
CHOH1907
DASP253
DGLN257
DLYS260
CLYS72
CALA74
CTHR75
CILE76
CTHR77
CARG82
CASN96
CLEU288
CALA308
CHIS309
CGLY310
CTHR311
CVAL312
CTHR313
CARG314
CHIS315

site_idAC8
Number of Residues27
DetailsBINDING SITE FOR RESIDUE NAP D 1518
ChainResidue
CASP253
CGLN257
CLYS260
DLYS72
DALA74
DTHR75
DILE76
DTHR77
DARG82
DASN96
DLEU288
DALA307
DALA308
DHIS309
DGLY310
DTHR311
DVAL312
DTHR313
DARG314
DHIS315
DASN328
DICT1619
DHOH1748
DHOH1771
DHOH1825
DHOH1826
DHOH1922

site_idAC9
Number of Residues13
DetailsBINDING SITE FOR RESIDUE ICT A 1616
ChainResidue
ATHR77
ASER94
AARG100
AARG109
AARG132
ATYR139
AASP275
ANAP1515
ACA1717
BLYS212
BTHR214
BASP252
BHOH1886

site_idBC1
Number of Residues12
DetailsBINDING SITE FOR RESIDUE ICT B 1617
ChainResidue
ALYS212
ATHR214
AASP252
BTHR77
BSER94
BARG100
BARG109
BARG132
BTYR139
BASP275
BNAP1516
BCA1718

site_idBC2
Number of Residues13
DetailsBINDING SITE FOR RESIDUE ICT C 1618
ChainResidue
CTHR77
CSER94
CARG100
CARG109
CARG132
CTYR139
CASP275
CNAP1517
CCA1719
DLYS212
DTHR214
DILE215
DASP252

site_idBC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE ICT D 1619
ChainResidue
CLYS212
CTHR214
CASP252
DTHR77
DSER94
DARG100
DARG109
DARG132
DTYR139
DASP275
DNAP1518
DCA1720
DHOH1767

Functional Information from PROSITE/UniProt
site_idPS00470
Number of Residues20
DetailsIDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NYDGDVqSDsvAqgy.GSLGM
ChainResidueDetails
AASN271-MET290

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T09, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM, ECO:0007744|PDB:3MAP, ECO:0007744|PDB:3MAR, ECO:0007744|PDB:3MAS, ECO:0007744|PDB:4I3K, ECO:0007744|PDB:4I3L, ECO:0007744|PDB:4KZO, ECO:0007744|PDB:4L03, ECO:0007744|PDB:4L04, ECO:0007744|PDB:4L06, ECO:0007744|PDB:4UMX, ECO:0007744|PDB:4UMY, ECO:0007744|PDB:4XRX, ECO:0007744|PDB:4XS3, ECO:0007744|PDB:5DE1, ECO:0007744|PDB:5L57, ECO:0007744|PDB:5L58, ECO:0007744|PDB:5LGE, ECO:0007744|PDB:5SUN, ECO:0007744|PDB:5SVF, ECO:0007744|PDB:5TQH
ChainResidueDetails
ATHR75
DTHR75
DGLY310
DASN328
AGLY310
AASN328
BTHR75
BGLY310
BASN328
CTHR75
CGLY310
CASN328

site_idSWS_FT_FI2
Number of Residues16
DetailsBINDING: in other chain => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L
ChainResidueDetails
ATHR77
CSER94
CARG109
CARG132
DTHR77
DSER94
DARG109
DARG132
ASER94
AARG109
AARG132
BTHR77
BSER94
BARG109
BARG132
CTHR77

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T09, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM, ECO:0007744|PDB:3MAP, ECO:0007744|PDB:3MAR, ECO:0007744|PDB:3MAS, ECO:0007744|PDB:4I3K, ECO:0007744|PDB:4I3L, ECO:0007744|PDB:4KZO, ECO:0007744|PDB:4L03, ECO:0007744|PDB:4L04, ECO:0007744|PDB:4L06, ECO:0007744|PDB:4UMX, ECO:0007744|PDB:4UMY, ECO:0007744|PDB:4XRX, ECO:0007744|PDB:4XS3, ECO:0007744|PDB:5DE1, ECO:0007744|PDB:5L57, ECO:0007744|PDB:5LGE, ECO:0007744|PDB:5SUN, ECO:0007744|PDB:5SVF, ECO:0007744|PDB:5TQH
ChainResidueDetails
AARG82
BARG82
CARG82
DARG82

site_idSWS_FT_FI4
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L
ChainResidueDetails
ALYS212
BLYS212
CLYS212
DLYS212

site_idSWS_FT_FI5
Number of Residues4
DetailsBINDING: BINDING => ECO:0000305|PubMed:15173171, ECO:0000305|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM
ChainResidueDetails
AASP252
BASP252
CASP252
DASP252

site_idSWS_FT_FI6
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM
ChainResidueDetails
ALYS260
BLYS260
CLYS260
DLYS260

site_idSWS_FT_FI7
Number of Residues8
DetailsBINDING: in other chain => ECO:0000305|PubMed:15173171, ECO:0000305|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM
ChainResidueDetails
AASP275
AASP279
BASP275
BASP279
CASP275
CASP279
DASP275
DASP279

site_idSWS_FT_FI8
Number of Residues8
DetailsSITE: Critical for catalysis
ChainResidueDetails
ATYR139
ALYS212
BTYR139
BLYS212
CTYR139
CLYS212
DTYR139
DLYS212

site_idSWS_FT_FI9
Number of Residues4
DetailsMOD_RES: N-acetylserine => ECO:0007744|PubMed:22814378
ChainResidueDetails
ASER2
BSER2
CSER2
DSER2

site_idSWS_FT_FI10
Number of Residues4
DetailsMOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569
ChainResidueDetails
ATYR42
BTYR42
CTYR42
DTYR42

site_idSWS_FT_FI11
Number of Residues16
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O88844
ChainResidueDetails
ALYS81
CLYS224
CLYS233
CLYS243
DLYS81
DLYS224
DLYS233
DLYS243
ALYS224
ALYS233
ALYS243
BLYS81
BLYS224
BLYS233
BLYS243
CLYS81

site_idSWS_FT_FI12
Number of Residues8
DetailsMOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:O88844
ChainResidueDetails
ALYS126
ALYS400
BLYS126
BLYS400
CLYS126
CLYS400
DLYS126
DLYS400

site_idSWS_FT_FI13
Number of Residues4
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
ALYS321
BLYS321
CLYS321
DLYS321

site_idSWS_FT_FI14
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O88844
ChainResidueDetails
ASER389
BSER389
CSER389
DSER389

Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
AVAL146

site_idCSA2
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
BVAL146

site_idCSA3
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
CVAL146

site_idCSA4
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
DVAL146

site_idCSA5
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
ALYS212
AASP252

site_idCSA6
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
BLYS212
BASP252

site_idCSA7
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
CLYS212
CASP252

site_idCSA8
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
DLYS212
DASP252

site_idCSA9
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
ATHR155

site_idCSA10
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
BTHR155

site_idCSA11
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
CTHR155

site_idCSA12
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
DTHR155

219140

PDB entries from 2024-05-01

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