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(-) Description

Title :  STRUCTURE OF IDH2 MUTANT R172K
 
Authors :  X. Xie, R. Kulathila
Date :  06 Aug 16  (Deposition) - 08 Feb 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Isocitrate Dehydrogenase, Mitochondrial, Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Xie, D. Baird, K. Bowen, V. Capka, J. Chen, G. Chenail, Y. Cho, J. Dooley, A. Farsidjani, P. Fortin, D. Kohls, R. Kulathila, F. Lin, D. Mckay, L. Rodrigues, D. Sage, B. B. Toure, S. Van Der Plas, K. Wright, M. Xu, H. Yin, J. Levell, R. A. Pagliarini
Allosteric Mutant Idh1 Inhibitors Reveal Mechanisms For Idh Mutant And Isoform Selectivity.
Structure V. 25 506 2017
PubMed-ID: 28132785  |  Reference-DOI: 10.1016/J.STR.2016.12.017

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL
    ChainsA, B
    EC Number1.1.1.42
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneIDH2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIDH,ICD-M,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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:112 , ALA A:114 , THR A:115 , ILE A:116 , THR A:117 , ARG A:122 , ASN A:136 , HIS A:348 , GLY A:349 , THR A:350 , VAL A:351 , THR A:352 , HIS A:354 , ASN A:367 , ASP A:414 , HOH A:603 , HOH A:612 , HOH A:617 , HOH A:623 , HOH A:641 , HOH A:650 , HOH A:660 , HOH A:667 , HOH A:675 , HOH A:682 , LEU B:289 , ASP B:292 , GLN B:296 , LYS B:299 , HOH B:667binding site for residue NDP A 501
2AC2SOFTWAREPRO A:245 , TYR A:247 , GLY A:303 , HOH A:604 , HOH A:626binding site for residue PEG A 502
3AC3SOFTWARELEU A:289 , ASP A:292 , GLN A:296 , LYS A:299 , HOH A:653 , HOH A:665 , LYS B:112 , ALA B:114 , THR B:115 , ILE B:116 , THR B:117 , ARG B:122 , ASN B:136 , HIS B:348 , GLY B:349 , THR B:350 , VAL B:351 , THR B:352 , HIS B:354 , THR B:366 , ASN B:367 , HOH B:603 , HOH B:624 , HOH B:625 , HOH B:631 , HOH B:639 , HOH B:641 , HOH B:651 , HOH B:669binding site for residue NDP B 501
4AC4SOFTWARETYR B:247 , GLY B:302binding site for residue PEG B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5SVN)

(-) 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:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeeee..hhhhhheeeee...eeeeeeeee......eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhh....eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5svn A  43 RIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDIQLKYFDLGLPNRDQTDDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPITIGKHAHGDQYKATDFVADRAGTFKMVFTPKDGSGVKEWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFDKHYKTDFDKNKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQMLEKVCVETVESGAMTKDLAGCIHGFLNTTDFLDTIKSNLDRALG 450
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       431       441         
                                                                                                                                                                                                                                                                                                                                                                                                                    421|                   
                                                                                                                                                                                                                                                                                                                                                                                                                     431                   

Chain B from PDB  Type:PROTEIN  Length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeeee.hhhhhhhhhhhhhhh....ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeeee..hhhhhheeeee...eeeeeeeee......eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh....eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5svn B  43 RIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDIQLKYFDLGLPNRDQTDDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPITIGKHAHGDQYKATDFVADRAGTFKMVFTPKDGSGVKEWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFDKHYKTDFDKNKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQMLEKVCVETVESGAMTKDLAGCIHGLSNLNEHFLNTTDFLDTIKSNLDRALGR 451
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422 ||    434       444       
                                                                                                                                                                                                                                                                                                                                                                                                                       424|                        
                                                                                                                                                                                                                                                                                                                                                                                                                        427                        

   Legend:   → Mismatch (orange background)
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  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 5SVN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IDHP_HUMAN | P487354ja8 5gis 5i95 5i96 5svo

(-) Related Entries Specified in the PDB File

5sun 5SUN CONTAINS A DIFFERENT ISOFORM OF THE PROTEIN
5svf
5svo