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3BLW

Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0003723molecular_functionRNA binding
A0003824molecular_functioncatalytic activity
A0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
A0005515molecular_functionprotein binding
A0005739cellular_componentmitochondrion
A0005758cellular_componentmitochondrial intermembrane space
A0005759cellular_componentmitochondrial matrix
A0005829cellular_componentcytosol
A0006099biological_processtricarboxylic acid cycle
A0006102biological_processisocitrate metabolic process
A0006537biological_processglutamate biosynthetic process
A0016491molecular_functionoxidoreductase activity
A0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A0042645cellular_componentmitochondrial nucleoid
A0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
A0046872molecular_functionmetal ion binding
A0051287molecular_functionNAD binding
B0000287molecular_functionmagnesium ion binding
B0003723molecular_functionRNA binding
B0003824molecular_functioncatalytic activity
B0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
B0005515molecular_functionprotein binding
B0005739cellular_componentmitochondrion
B0005759cellular_componentmitochondrial matrix
B0006099biological_processtricarboxylic acid cycle
B0006102biological_processisocitrate metabolic process
B0006537biological_processglutamate biosynthetic process
B0016491molecular_functionoxidoreductase activity
B0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
B0046872molecular_functionmetal ion binding
B0051287molecular_functionNAD binding
C0000287molecular_functionmagnesium ion binding
C0003723molecular_functionRNA binding
C0003824molecular_functioncatalytic activity
C0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
C0005515molecular_functionprotein binding
C0005739cellular_componentmitochondrion
C0005758cellular_componentmitochondrial intermembrane space
C0005759cellular_componentmitochondrial matrix
C0005829cellular_componentcytosol
C0006099biological_processtricarboxylic acid cycle
C0006102biological_processisocitrate metabolic process
C0006537biological_processglutamate biosynthetic process
C0016491molecular_functionoxidoreductase activity
C0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C0042645cellular_componentmitochondrial nucleoid
C0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
C0046872molecular_functionmetal ion binding
C0051287molecular_functionNAD binding
D0000287molecular_functionmagnesium ion binding
D0003723molecular_functionRNA binding
D0003824molecular_functioncatalytic activity
D0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
D0005515molecular_functionprotein binding
D0005739cellular_componentmitochondrion
D0005759cellular_componentmitochondrial matrix
D0006099biological_processtricarboxylic acid cycle
D0006102biological_processisocitrate metabolic process
D0006537biological_processglutamate biosynthetic process
D0016491molecular_functionoxidoreductase activity
D0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
D0046872molecular_functionmetal ion binding
D0051287molecular_functionNAD binding
E0000287molecular_functionmagnesium ion binding
E0003723molecular_functionRNA binding
E0003824molecular_functioncatalytic activity
E0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
E0005515molecular_functionprotein binding
E0005739cellular_componentmitochondrion
E0005758cellular_componentmitochondrial intermembrane space
E0005759cellular_componentmitochondrial matrix
E0005829cellular_componentcytosol
E0006099biological_processtricarboxylic acid cycle
E0006102biological_processisocitrate metabolic process
E0006537biological_processglutamate biosynthetic process
E0016491molecular_functionoxidoreductase activity
E0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E0042645cellular_componentmitochondrial nucleoid
E0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
E0046872molecular_functionmetal ion binding
E0051287molecular_functionNAD binding
F0000287molecular_functionmagnesium ion binding
F0003723molecular_functionRNA binding
F0003824molecular_functioncatalytic activity
F0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
F0005515molecular_functionprotein binding
F0005739cellular_componentmitochondrion
F0005759cellular_componentmitochondrial matrix
F0006099biological_processtricarboxylic acid cycle
F0006102biological_processisocitrate metabolic process
F0006537biological_processglutamate biosynthetic process
F0016491molecular_functionoxidoreductase activity
F0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
F0046872molecular_functionmetal ion binding
F0051287molecular_functionNAD binding
G0000287molecular_functionmagnesium ion binding
G0003723molecular_functionRNA binding
G0003824molecular_functioncatalytic activity
G0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
G0005515molecular_functionprotein binding
G0005739cellular_componentmitochondrion
G0005758cellular_componentmitochondrial intermembrane space
G0005759cellular_componentmitochondrial matrix
G0005829cellular_componentcytosol
G0006099biological_processtricarboxylic acid cycle
G0006102biological_processisocitrate metabolic process
G0006537biological_processglutamate biosynthetic process
G0016491molecular_functionoxidoreductase activity
G0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
G0042645cellular_componentmitochondrial nucleoid
G0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
G0046872molecular_functionmetal ion binding
G0051287molecular_functionNAD binding
H0000287molecular_functionmagnesium ion binding
H0003723molecular_functionRNA binding
H0003824molecular_functioncatalytic activity
H0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
H0005515molecular_functionprotein binding
H0005739cellular_componentmitochondrion
H0005759cellular_componentmitochondrial matrix
H0006099biological_processtricarboxylic acid cycle
H0006102biological_processisocitrate metabolic process
H0006537biological_processglutamate biosynthetic process
H0016491molecular_functionoxidoreductase activity
H0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
H0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
H0046872molecular_functionmetal ion binding
H0051287molecular_functionNAD binding
I0000287molecular_functionmagnesium ion binding
I0003723molecular_functionRNA binding
I0003824molecular_functioncatalytic activity
I0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
I0005515molecular_functionprotein binding
I0005739cellular_componentmitochondrion
I0005758cellular_componentmitochondrial intermembrane space
I0005759cellular_componentmitochondrial matrix
I0005829cellular_componentcytosol
I0006099biological_processtricarboxylic acid cycle
I0006102biological_processisocitrate metabolic process
I0006537biological_processglutamate biosynthetic process
I0016491molecular_functionoxidoreductase activity
I0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
I0042645cellular_componentmitochondrial nucleoid
I0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
I0046872molecular_functionmetal ion binding
I0051287molecular_functionNAD binding
J0000287molecular_functionmagnesium ion binding
J0003723molecular_functionRNA binding
J0003824molecular_functioncatalytic activity
J0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
J0005515molecular_functionprotein binding
J0005739cellular_componentmitochondrion
J0005759cellular_componentmitochondrial matrix
J0006099biological_processtricarboxylic acid cycle
J0006102biological_processisocitrate metabolic process
J0006537biological_processglutamate biosynthetic process
J0016491molecular_functionoxidoreductase activity
J0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
J0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
J0046872molecular_functionmetal ion binding
J0051287molecular_functionNAD binding
K0000287molecular_functionmagnesium ion binding
K0003723molecular_functionRNA binding
K0003824molecular_functioncatalytic activity
K0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
K0005515molecular_functionprotein binding
K0005739cellular_componentmitochondrion
K0005758cellular_componentmitochondrial intermembrane space
K0005759cellular_componentmitochondrial matrix
K0005829cellular_componentcytosol
K0006099biological_processtricarboxylic acid cycle
K0006102biological_processisocitrate metabolic process
K0006537biological_processglutamate biosynthetic process
K0016491molecular_functionoxidoreductase activity
K0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
K0042645cellular_componentmitochondrial nucleoid
K0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
K0046872molecular_functionmetal ion binding
K0051287molecular_functionNAD binding
L0000287molecular_functionmagnesium ion binding
L0003723molecular_functionRNA binding
L0003824molecular_functioncatalytic activity
L0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
L0005515molecular_functionprotein binding
L0005739cellular_componentmitochondrion
L0005759cellular_componentmitochondrial matrix
L0006099biological_processtricarboxylic acid cycle
L0006102biological_processisocitrate metabolic process
L0006537biological_processglutamate biosynthetic process
L0016491molecular_functionoxidoreductase activity
L0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
L0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
L0046872molecular_functionmetal ion binding
L0051287molecular_functionNAD binding
M0000287molecular_functionmagnesium ion binding
M0003723molecular_functionRNA binding
M0003824molecular_functioncatalytic activity
M0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
M0005515molecular_functionprotein binding
M0005739cellular_componentmitochondrion
M0005758cellular_componentmitochondrial intermembrane space
M0005759cellular_componentmitochondrial matrix
M0005829cellular_componentcytosol
M0006099biological_processtricarboxylic acid cycle
M0006102biological_processisocitrate metabolic process
M0006537biological_processglutamate biosynthetic process
M0016491molecular_functionoxidoreductase activity
M0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
M0042645cellular_componentmitochondrial nucleoid
M0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
M0046872molecular_functionmetal ion binding
M0051287molecular_functionNAD binding
N0000287molecular_functionmagnesium ion binding
N0003723molecular_functionRNA binding
N0003824molecular_functioncatalytic activity
N0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
N0005515molecular_functionprotein binding
N0005739cellular_componentmitochondrion
N0005759cellular_componentmitochondrial matrix
N0006099biological_processtricarboxylic acid cycle
N0006102biological_processisocitrate metabolic process
N0006537biological_processglutamate biosynthetic process
N0016491molecular_functionoxidoreductase activity
N0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
N0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
N0046872molecular_functionmetal ion binding
N0051287molecular_functionNAD binding
O0000287molecular_functionmagnesium ion binding
O0003723molecular_functionRNA binding
O0003824molecular_functioncatalytic activity
O0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
O0005515molecular_functionprotein binding
O0005739cellular_componentmitochondrion
O0005758cellular_componentmitochondrial intermembrane space
O0005759cellular_componentmitochondrial matrix
O0005829cellular_componentcytosol
O0006099biological_processtricarboxylic acid cycle
O0006102biological_processisocitrate metabolic process
O0006537biological_processglutamate biosynthetic process
O0016491molecular_functionoxidoreductase activity
O0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
O0042645cellular_componentmitochondrial nucleoid
O0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
O0046872molecular_functionmetal ion binding
O0051287molecular_functionNAD binding
P0000287molecular_functionmagnesium ion binding
P0003723molecular_functionRNA binding
P0003824molecular_functioncatalytic activity
P0004449molecular_functionisocitrate dehydrogenase (NAD+) activity
P0005515molecular_functionprotein binding
P0005739cellular_componentmitochondrion
P0005759cellular_componentmitochondrial matrix
P0006099biological_processtricarboxylic acid cycle
P0006102biological_processisocitrate metabolic process
P0006537biological_processglutamate biosynthetic process
P0016491molecular_functionoxidoreductase activity
P0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
P0045242cellular_componentisocitrate dehydrogenase complex (NAD+)
P0046872molecular_functionmetal ion binding
P0051287molecular_functionNAD binding
Functional Information from PDB Data
site_idAC1
Number of Residues10
DetailsBINDING SITE FOR RESIDUE FLC A 1001
ChainResidue
ATHR83
BLYS189
ASER92
AASN94
AVAL95
AARG98
AARG129
APHE136
ATHR241
AARG274

site_idAC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE FLC C 1002
ChainResidue
CTHR83
CSER92
CASN94
CVAL95
CARG98
CARG129
CPHE136
CTHR241
CARG274
DLYS189

site_idAC3
Number of Residues10
DetailsBINDING SITE FOR RESIDUE FLC E 1003
ChainResidue
ETHR83
ESER92
EARG98
EARG129
EPHE136
ETHR241
EARG274
FLYS189
FTHR191
FASP222

site_idAC4
Number of Residues10
DetailsBINDING SITE FOR RESIDUE FLC G 1004
ChainResidue
GTHR83
GSER92
GVAL95
GARG98
GARG129
GPHE136
GTHR241
GARG274
HLYS189
HTHR191

site_idAC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE FLC I 1005
ChainResidue
ITHR83
ISER92
IVAL95
IARG98
IARG129
IPHE136
ITHR241
IARG274
JLYS189

site_idAC6
Number of Residues9
DetailsBINDING SITE FOR RESIDUE FLC K 1006
ChainResidue
KTHR83
KSER92
KARG98
KARG129
KPHE136
KTHR241
KARG274
LLYS189
LASP222

site_idAC7
Number of Residues9
DetailsBINDING SITE FOR RESIDUE FLC M 1007
ChainResidue
MTHR83
MSER92
MASN94
MVAL95
MARG98
MPHE136
MTHR241
MARG274
NLYS189

site_idAC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE FLC O 1008
ChainResidue
OTHR83
OSER92
OASN94
OARG98
OARG129
OPHE136
OTHR241
OARG274
PLYS189

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE AMP A 2001
ChainResidue
AHIS275
AGLY277
AALA286
AASN287
AASP328
BASN223

site_idBC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE AMP C 2002
ChainResidue
CVAL28
CILE32
CGLY255
CHIS275
CVAL276
CGLY277
CASN287
DASN223

site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE AMP E 2003
ChainResidue
EVAL28
EHIS275
EGLY277
EASN287
FASN223

site_idBC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AMP G 2004
ChainResidue
GASN287
GASP328
HASN223
GVAL28
GHIS275
GGLY277
GALA286

site_idBC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE AMP I 2005
ChainResidue
IHIS275
IGLY277
IALA286
IASN287
IASP328
JASN223

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE AMP K 2006
ChainResidue
KVAL28
KHIS275
KVAL276
KGLY277
KALA286
LASN223

site_idBC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE AMP M 2007
ChainResidue
MILE32
MGLY255
MHIS275
MVAL276
MGLY277
MASP279
MASN287
NASN223

site_idBC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AMP O 2008
ChainResidue
OVAL28
OHIS275
OVAL276
OGLY277
OASN287
OASP328
PASN223

Functional Information from PROSITE/UniProt
site_idPS00470
Number of Residues20
DetailsIDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. SMYGTIlGNigAali.GGPGL
ChainResidueDetails
ASER237-LEU256
BASN244-LEU264

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues56
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues24
DetailsSite: {"description":"Critical for catalysis","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues16
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"P50213","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues8
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues8
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues8
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues8
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17761666","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
BTYR142

site_idCSA10
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
CPHE136

site_idCSA11
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
EPHE136

site_idCSA12
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
GPHE136

site_idCSA13
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
IPHE136

site_idCSA14
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
KPHE136

site_idCSA15
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
MPHE136

site_idCSA16
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
OPHE136

site_idCSA17
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
BLYS189
BASP222

site_idCSA18
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
DLYS189
DASP222

site_idCSA19
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
FLYS189
FASP222

site_idCSA2
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
DTYR142

site_idCSA20
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
HLYS189
HASP222

site_idCSA21
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
JLYS189
JASP222

site_idCSA22
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
LLYS189
LASP222

site_idCSA23
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
NLYS189
NASP222

site_idCSA24
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
PLYS189
PASP222

site_idCSA25
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
ALYS183
AASP217

site_idCSA26
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
CLYS183
CASP217

site_idCSA27
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
ELYS183
EASP217

site_idCSA28
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
GLYS183
GASP217

site_idCSA29
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
ILYS183
IASP217

site_idCSA3
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
FTYR142

site_idCSA30
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
KLYS183
KASP217

site_idCSA31
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
MLYS183
MASP217

site_idCSA32
Number of Residues2
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
OLYS183
OASP217

site_idCSA4
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
HTYR142

site_idCSA5
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
JTYR142

site_idCSA6
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
LTYR142

site_idCSA7
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
NTYR142

site_idCSA8
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
PTYR142

site_idCSA9
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a05
ChainResidueDetails
APHE136

246704

PDB entries from 2025-12-24

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