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5YZH

Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase

Replaces:  2CMJ
Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0004450molecular_functionisocitrate dehydrogenase (NADP+) activity
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
A0006740biological_processNADPH regeneration
A0006749biological_processglutathione metabolic process
A0006979biological_processresponse to oxidative stress
A0008585biological_processfemale gonad development
A0016491molecular_functionoxidoreductase activity
A0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A0042802molecular_functionidentical protein binding
A0042803molecular_functionprotein homodimerization activity
A0046872molecular_functionmetal ion binding
A0048545biological_processresponse to steroid hormone
A0050661molecular_functionNADP binding
A0051287molecular_functionNAD binding
A0060696biological_processregulation of phospholipid catabolic process
A0071071biological_processregulation of phospholipid biosynthetic process
B0000287molecular_functionmagnesium ion binding
B0004450molecular_functionisocitrate dehydrogenase (NADP+) activity
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
B0006740biological_processNADPH regeneration
B0006749biological_processglutathione metabolic process
B0006979biological_processresponse to oxidative stress
B0008585biological_processfemale gonad development
B0016491molecular_functionoxidoreductase activity
B0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B0042802molecular_functionidentical protein binding
B0042803molecular_functionprotein homodimerization activity
B0046872molecular_functionmetal ion binding
B0048545biological_processresponse to steroid hormone
B0050661molecular_functionNADP binding
B0051287molecular_functionNAD binding
B0060696biological_processregulation of phospholipid catabolic process
B0071071biological_processregulation of phospholipid biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues35
Detailsbinding site for residue NAP A 501
ChainResidue
ALYS72
ATHR311
AVAL312
ATHR313
AARG314
AHIS315
AASN328
AHOH601
AHOH619
AHOH625
AHOH633
AALA74
AHOH647
AHOH672
AHOH724
AHOH728
AHOH748
AHOH749
AHOH775
AHOH780
AHOH824
BLEU250
ATHR75
BASP253
BGLN257
BLYS260
BHOH625
BHOH669
BHOH700
AILE76
ATHR77
AARG82
AASN96
AHIS309
AGLY310

site_idAC2
Number of Residues5
Detailsbinding site for residue GOL A 502
ChainResidue
APRO206
AGLU262
AGLY263
AGLY264
AHOH777

site_idAC3
Number of Residues33
Detailsbinding site for residue NAP B 501
ChainResidue
AASP253
AGLN257
ALYS260
AHOH642
AHOH689
BLYS72
BALA74
BTHR75
BTHR77
BARG82
BASN96
BALA307
BHIS309
BGLY310
BTHR311
BVAL312
BTHR313
BARG314
BHIS315
BASN328
BHOH606
BHOH621
BHOH624
BHOH632
BHOH644
BHOH646
BHOH692
BHOH702
BHOH715
BHOH730
BHOH734
BHOH735
BHOH767

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 Residues20
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"29923039","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5YZH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5YZI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues18
DetailsBinding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"29923039","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5YZI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"29923039","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5YZI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"29923039","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsBinding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"29923039","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues4
DetailsSite: {"description":"Critical for catalysis","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"O75874","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues8
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"23576753","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"PubMed","id":"23806337","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"O75874","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"21183079","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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