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(-) Description

Title :  NMR STRUCTURE OF A COMPLEX BETWEEN MDM2 AND A SMALL MOLECULE INHIBITOR
 
Authors :  D. C. Fry, S. D. Emerson, S. Palme, B. T. Vu, C. M. Liu, F. Podlaski
Date :  23 Jun 04  (Deposition) - 04 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (18x)
Keywords :  Mdm2, Protein-Protein Interaction, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Fry, S. D. Emerson, S. Palme, B. T. Vu, C. M. Liu, F. Podlaski
Nmr Structure Of A Complex Between Mdm2 And A Small Molecule Inhibitor.
J. Biomol. Nmr V. 30 163 2004
PubMed-ID: 15557803  |  Reference-DOI: 10.1023/B:JNMR.0000048856.84603.9B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-PROTEIN LIGASE E3 MDM2
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PUBS 520
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIUDES 13-119
    Gene: MDM2
    Mutation: YES
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: P53-BINDING PROTEIN MDM2, DOUBLE MINUTE 2 PROTEIN, XDM2

 Structural Features

(-) Chains, Units

  
NMR Structure (18x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1IMY1Ligand/Ion1-{[4,5-BIS(4-CHLOROPHENYL)-2-(2-ISOPROPOXY-4-METHOXYPHENYL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]CARBONYL}PIPERAZINE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:50 , LEU A:53 , GLY A:54 , ILE A:57 , GLN A:68 , HIS A:69 , VAL A:89 , HIS A:92BINDING SITE FOR RESIDUE IMY A 120

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TTV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TTV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TTV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TTV)

(-) Exons   (0, 0)

(no "Exon" information available for 1TTV)

(-) Sequences/Alignments

NMR Structure
   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:107
 aligned with MDM2_XENLA | P56273 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:107
                                    22        32        42        52        62        72        82        92       102       112       
           MDM2_XENLA    13 NHISTSDQEKLVQPTPLLLSLLKSAGAQKETFTMKEVIYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEPRRLYAMISRNLVSANVKESSEDIFGNV 119
               SCOP domains d1ttva_ A: MDM2                                                                                             SCOP domains
               CATH domains 1ttvA00 A:13-119 MDM2                                                                                       CATH domains
               Pfam domains ----------SWIB-1ttvA01 A:23-98                                                        --------------------- Pfam domains
         Sec.struct. author ...........eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........ee....hhhhhhhh...ee..hhhhhhhhhhh.eeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1ttv A  13 NHISTSDQEKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLVSANVKESSEDIFGNV 119
                                    22        32        42        52        62        72        82        92       102       112
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: SWIB] (22)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (MDM2_XENLA | P56273)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0071157    negative regulation of cell cycle arrest    Any process that decreases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MDM2_XENLA | P56273: 1ycq 4ipf 4j3e 4j74 4j7d 4j7e 4jrg 4jsc 4lwt 4lwu 4lwv

(-) Related Entries Specified in the PDB File

1rv1 X-RAY STRUCTURE OF MDM2 WITH AN IMIDAZOLINE INHIBITOR BY LUKACS, KAMMLOTT, AND GRAVES
1ycq X-RAY STRUCTURE OF MDM2 WITH A P53 PEPTIDE BY KUSSIE ET AL.