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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE CYTOSOLIC ISOCITRATE DEHYDROGENASE COMPLEXED WITH CADMIUM AND CITRATE
 
Authors :  H. J. Cho, K. J. Kim, T. L. Huh, B. S. Kang
Date :  15 May 06  (Deposition) - 29 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tricarboxylic Acid Cycle, Isocitrate Dehydrogenase, Nadp, Cadmium, Oxidoreductase, Glyoxylate Bypass (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. J. Cho, K. J. Kim, T. L. Huh, B. S. Kang
Crystal Structure Of Mouse Cytosolic Isocitrate Dehydrogenase Complexed With Cadmium And Citrate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
    ChainsA, B
    EC Number1.1.1.42
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantDE3
    FragmentRESIDUES 4-413
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymOXALOSUCCINATE DECARBOXYLASE, IDH, NADP, +-SPECIFIC ICDH), IDP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2FLC2Ligand/IonCITRATE ANION
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:275 , ASP A:279 , FLC A:1416 , HOH A:2022 , HOH A:2051 , ASP B:252BINDING SITE FOR RESIDUE CD A1414
2AC2SOFTWARETHR A:77 , SER A:94 , ASN A:96 , ARG A:100 , ARG A:109 , ARG A:132 , TYR A:139 , ASP A:275 , CD A:1414 , NAP A:1415 , HOH A:2022 , LYS B:212 , ILE B:215 , ASP B:252BINDING SITE FOR RESIDUE FLC A1416
3AC3SOFTWAREASP A:252 , ASP B:275 , ASP B:279 , FLC B:1416BINDING SITE FOR RESIDUE CD B1414
4AC4SOFTWARELYS A:212 , ILE A:215 , ASP A:252 , THR B:77 , SER B:94 , ASN B:96 , ARG B:100 , ARG B:109 , ARG B:132 , TYR B:139 , ASP B:275 , ALA B:308 , CD B:1414 , NAP B:1415 , HOH B:2048BINDING SITE FOR RESIDUE FLC B1416
5AC5SOFTWARELYS A:72 , ALA A:74 , THR A:75 , THR A:77 , ARG A:82 , ASN A:96 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , ASN A:328 , FLC A:1416 , HOH A:2064 , HOH A:2065 , HOH A:2066 , HOH A:2067 , HOH A:2068 , ASP B:253 , GLN B:257 , LYS B:260 , HOH B:2032BINDING SITE FOR RESIDUE NAP A1415
6AC6SOFTWARELYS A:260 , LYS B:72 , ALA B:74 , THR B:75 , THR B:77 , ASN B:96 , LEU B:288 , GLU B:306 , HIS B:309 , GLY B:310 , THR B:311 , VAL B:312 , THR B:313 , ARG B:314 , ASN B:328 , FLC B:1416 , HOH B:2047BINDING SITE FOR RESIDUE NAP B1415

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CMV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CMV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CMV)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.IDHC_MOUSE271-290
 
  2A:271-290
B:271-290

(-) Exons   (0, 0)

(no "Exon" information available for 2CMV)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:410
 aligned with IDHC_MOUSE | O88844 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:410
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
           IDHC_MOUSE     4 KIQGGSVVEMQGDEMTRIIWELIKEKLILPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVTGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPKDGTQKVTYMVHDFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKKYKSQFEAQKICYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLICPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWSRGLAHRAKLDNNTELSFFAKALEDVCIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKAKLAQAK 413
               SCOP domains d2cmva_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cmvA00 A:4-413 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cmv A   4 KIQGGSVVEMQGDEMTRIIWELIKEKLILPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVTGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPKDGTQKVTYMVHDFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKKYKSQFEAQNICYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLICPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWSRGLAHRAKLDNNTELSFFAKALEDVCIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKAKLAQAK 413
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413

Chain B from PDB  Type:PROTEIN  Length:409
 aligned with IDHC_MOUSE | O88844 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:409
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403         
           IDHC_MOUSE     4 KIQGGSVVEMQGDEMTRIIWELIKEKLILPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVTGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPKDGTQKVTYMVHDFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKKYKSQFEAQKICYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLICPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWSRGLAHRAKLDNNTELSFFAKALEDVCIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKAKLAQA 412
               SCOP domains d2cmvb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2cmvB00 B:4-412 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhh....eeeeee......eee......hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cmv B   4 KIQGGSVVEMQGDEMTRIIWELIKEKLILPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKYNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVTGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPKDGTQKVTYMVHDFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKKYKSQFEAQNICYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLICPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWSRGLAHRAKLDNNTELSFFAKALEDVCIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKAKLAQA 412
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CMV)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IDHC_MOUSE | O88844)
molecular function
    GO:0051990    (R)-2-hydroxyglutarate dehydrogenase activity    Catalysis of the reaction: (R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004450    isocitrate dehydrogenase (NADP+) activity    Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+.
    GO:0004448    isocitrate dehydrogenase activity    Catalysis of the reaction: isocitrate + acceptor = 2-oxoglutarate + CO2 + reduced acceptor.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0006103    2-oxoglutarate metabolic process    The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
    GO:0008585    female gonad development    The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:0006097    glyoxylate cycle    A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
    GO:0006102    isocitrate metabolic process    The chemical reactions and pathways involving isocitrate, the anion of isocitric acid, 1-hydroxy-1,2,3-propanetricarboxylic acid. Isocitrate is an important intermediate in the TCA cycle and the glycoxylate cycle.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0071071    regulation of phospholipid biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phospholipids.
    GO:0060696    regulation of phospholipid catabolic process    Any process that modulates the rate, frequency, or extent of phospholipid catabolism, the chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0048545    response to steroid hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IDHC_MOUSE | O888442cmj

(-) Related Entries Specified in the PDB File

2cmj CRYSTAL STRUCTURE OF MOUSE CYTOSOLIC ISOCITRATE DEHYDROGENASE