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(-) Description

Title :  CRYSTAL STRUCTURE OF A METABOLIC REDUCTASE WITH 1-HYDROXY-6-(4-HYDROXYBENZYL)-4-METHYLPYRIDIN-2(1H)-ONE
 
Authors :  B. Zheng, Y. Yao, Z. Liu, L. Deng, J. L. Anglin, H. Jiang, B. V. V. Prasad, Y
Date :  26 Nov 12  (Deposition) - 22 May 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isocitrate Dehydrogenase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Zheng, Y. Yao, Z. Liu, L. Deng, J. L. Anglin, H. Jiang, B. V. Prasad, Y. Song
Crystallographic Investigation And Selective Inhibition Of Mutant Isocitrate Dehydrogenase.
Acs Med Chem Lett V. 4 542 2013
PubMed-ID: 23795241  |  Reference-DOI: 10.1021/ML400036Z

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: IDH1, PICD
    Mutation: YES
    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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
11BX1Ligand/Ion1-HYDROXY-6-(4-HYDROXYBENZYL)-4-METHYLPYRIDIN-2(1H)-ONE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:72 , ALA A:74 , THR A:75 , THR A:77 , ARG A:82 , ASN A:96 , GLU A:306 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , THR A:327 , ASN A:328 , 1BX A:505BINDING SITE FOR RESIDUE NDP A 501
2AC2SOFTWARELYS A:374BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARETHR A:313 , ARG A:317BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWAREHIS A:170 , ASN A:171 , GLU A:173 , GLU A:174 , GLY A:175 , GLN B:185BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWARETHR A:77 , SER A:94 , ASN A:96 , ARG A:100 , NDP A:501BINDING SITE FOR RESIDUE 1BX A 505
6AC6SOFTWARELYS B:72 , THR B:75 , ILE B:76 , THR B:77 , ARG B:82 , ASN B:96 , GLU B:306 , HIS B:309 , GLY B:310 , THR B:311 , VAL B:312 , THR B:313 , ARG B:314 , HIS B:315 , THR B:327 , ASN B:328BINDING SITE FOR RESIDUE NDP B 501
7AC7SOFTWARETHR B:313 , ARG B:317BINDING SITE FOR RESIDUE SO4 B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I3K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I3K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I3K)

(-) Exons   (0, 0)

(no "Exon" information available for 4I3K)

(-) 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:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee......eeeee..eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhh.eeeee.....eeeeee......eeeee....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3k A   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNPIIIGHHATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVGFIWACKNLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQ 411
                                    13        23        33        43        53        63        73        83        93       103       113  ||   133|      150       160       170       180       190       200       210       220       230       240       250    || 268  ||   294       304       314       324       334       344       354       364       374       384       394       404       
                                                                                                                                          116|   133|                                                                                                               255|    271|                                                                                                                           
                                                                                                                                           127    141                                                                                                                264     288                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee........eeee...eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhh.......eee.hhhhh...eeee.hhh.eeeeee......eeeee....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3k B   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPPIIIGHHATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSLKKYDGRFKDIFQEIYDKQYQKIWYEHRLIDDMEGGFIWACSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQ 411
                                    13        23        33        43        53        63        73        83        93       103       113    || 131 ||    148       158       168       178       188       198       208 ||    223       233 ||    249    || 266  ||   293       303       313       323       333       343       353       363       373       383       393       403        
                                                                                                                                            118|   133|                                                                  210|                235|         254|    269|                                                                                                                            
                                                                                                                                             127    141                                                                   216                 242          262     287
   Legend:   → Mismatch (orange background)
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  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 4I3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I3K)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        IDHC_HUMAN | O75874: 1t09 1t0l 3inm 3map 3mar 3mas 4i3l 4kzo 4l03 4l04 4l06 4umx 4umy 4xrx 4xs3 5de1 5gir 5k10 5k11 5l57 5l58 5lge 5sun 5svf 5tqh

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