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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALPHA GAMMA HETERODIMER OF HUMAN IDH3 IN COMPLEX WITH MG(2+), ISOCITRATE AND ADP
 
Authors :  T. Ma, J. Ding
Date :  11 Aug 16  (Deposition) - 15 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Allosteric Regulation, Isocitrate Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ma, Y. Peng, W. Huang, J. Ding
Molecular Mechanism Of The Allosteric Regulation Of The Alpha Gamma Heterodimer Of Human Nad-Dependent Isocitrate Dehydrogenase.
Sci Rep V. 7 40921 2017
PubMed-ID: 28098230  |  Reference-DOI: 10.1038/SREP40921

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL
    Chains: A
    EC Number: 1.1.1.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: IDH3A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ISOCITRIC DEHYDROGENASE SUBUNIT ALPHA,NAD(+)-SPECIFIC ICDH SUBUNIT ALPHA
 
Molecule 2 - ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL
    Chains: B
    EC Number: 1.1.1.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: IDH3G
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ISOCITRIC DEHYDROGENASE SUBUNIT GAMMA,NAD(+)-SPECIFIC ICDH SUBUNIT GAMMA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ICT1Ligand/IonISOCITRIC ACID
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:230 , ASP A:234 , ASP B:215binding site for residue MG A 401
2AC2SOFTWARETYR A:204 , ILE B:26 , ASN B:78 , PRO B:252 , ARG B:272 , ASN B:273 , THR B:274 , GLY B:275 , LYS B:276 , SER B:277 , ILE B:278 , ASN B:285 , ASP B:326 , MG B:403binding site for residue ADP B 401
3AC3SOFTWARELYS A:173 , ASN A:175 , ILE A:176 , ASN B:78 , SER B:91 , ASN B:93 , ARG B:97 , ARG B:128 , TYR B:135 , ASN B:239 , ARG B:272 , MG B:403binding site for residue ICT B 402
4AC4SOFTWAREASN B:78 , ARG B:272 , ADP B:401 , ICT B:402binding site for residue MG B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GRL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GRL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GRL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GRL)

(-) Exons   (0, 0)

(no "Exon" information available for 5GRL)

(-) 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:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhheeee......hhhhhhhhhhh..eeeeeee............eeeeeee.........eeeee..eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhh.hhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.hhh.eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5grl A   4 VQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQWMIPSEAKESMDKNKMGLKGPLKTPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACFATIKDGKSLTKDGGNAKCSDFTEEICRRVKDL 338
                                    13        23        33        43 ||     58        68     || 84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314  ||   325       335   
                                                                    45|                     74|                                                                                                                                                                                                                                         317|                   
                                                                     51                      81                                                                                                                                                                                                                                          319                   


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhheeee..............hhhhhhhhhh...eeeeeee............eeeeeee..hhhhh..eeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhh......eeeee....eeeee................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5grl B  15 RHTVTMIPGDGIGPELMLHVKSVFRHACVPVDFEEVHVSSNADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQESGRKKVTAVHKANIMKLGDGLFLQCCREVAARYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVLASMDNENMHTPDIGGQGTTSEAIQDVIRHIRVING 349
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344
   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  (0, 0)

(no "SCOP Domain" information available for 5GRL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GRL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GRL)

(-) Gene Ontology  (21, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  IDH3G_HUMAN | P51553
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 Related Entries

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

UniProtKB/Swiss-Prot
        IDH3A_HUMAN | P50213: 5gre 5grf 5grh 5gri
        IDH3G_HUMAN | P51553: 5gre 5grf 5grh 5gri

(-) Related Entries Specified in the PDB File

5gre 5grf 5grh 5gri