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(-) Description

Title :  CRYO-EM STRUCTURE OF ISOCITRATE DEHYDROGENASE (IDH1) IN INHIBITOR-BOUND STATE
 
Authors :  A. Merk, A. Bartesaghi, S. Banerjee, V. Falconieri, P. Rao, L. Earl, J. M S. Subramaniam
Date :  17 May 16  (Deposition) - 08 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isocitrate Dehydrogenase, Small Metabolic Complex, Small Molecule Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Merk, A. Bartesaghi, S. Banerjee, V. Falconieri, P. Rao, M. I. Davis R. Pragani, M. B. Boxer, L. A. Earl, J. L. Milne, S. Subramaniam
Breaking Cryo-Em Resolution Barriers To Facilitate Drug Discovery.
Cell V. 165 1698 2016
PubMed-ID: 27238019  |  Reference-DOI: 10.1016/J.CELL.2016.05.040

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Taxid: 10469
    Expression System Vector Type: BACULOVIRUS
    Gene: IDH1, PICD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IDH, CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE, IDP, NADP(+)- SPECIFIC ICDH, OXALOSUCCINATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:75 , ILE A:76 , THR A:77 , ARG A:82 , ASN A:96 , LEU A:288 , GLY A:289 , GLU A:306 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , ASN A:328 , ASP A:375binding site for residue NDP A 501
2AC2SOFTWARETHR B:75 , ILE B:76 , THR B:77 , ARG B:82 , ASN B:96 , LEU B:288 , GLY B:289 , GLU B:306 , HIS B:309 , GLY B:310 , THR B:311 , VAL B:312 , THR B:313 , ARG B:314 , HIS B:315 , ASN B:328 , ASP B:375binding site for residue NDP B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K11)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K11)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K11)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K11)

(-) Exons   (0, 0)

(no "Exon" information available for 5K11)

(-) 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:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhh.....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee.................eee....eeee.....eeeeeeeee......ee...eee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhh.hhhhhhhh....ee..hhhhhhhhhhhh....ee..............eeeeee......eeeee....hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k11 A   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGCHARATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAK 413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132 ||    147       157       167       177       187       197       207       217       227       237       247       257       267   ||  286       296       306       316       326       336       346       356       366       376       386       396       406       
                                                                                                                                                             134|                                                                                                                                271|                                                                                                                                    
                                                                                                                                                              140                                                                                                                                 281                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhh.....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee.................eee....eeee.....eeeeeeeee......ee...eee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhh.hhhhhhhh....ee..hhhhhhhhhhhh....ee..............eeeeee......eeeee....hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k11 B   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGCHARATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAK 413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132 ||    147       157       167       177       187       197       207       217       227       237       247       257       267   ||  286       296       306       316       326       336       346       356       366       376       386       396       406       
                                                                                                                                                             134|                                                                                                                                271|                                                                                                                                    
                                                                                                                                                              140                                                                                                                                 281
   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 5K11)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K11)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K11)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  5k11
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  IDHC_HUMAN | O75874
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  1.1.1.42
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 Related Entries

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

UniProtKB/Swiss-Prot
        IDHC_HUMAN | O75874: 1t09 1t0l 3inm 3map 3mar 3mas 4i3k 4i3l 4kzo 4l03 4l04 4l06 4umx 4umy 4xrx 4xs3 5de1 5gir 5k10 5l57 5l58 5lge 5sun 5svf 5tqh

(-) Related Entries Specified in the PDB File

5k0z 5k10 5k12