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(-) Description

Title :  THE 1.9A CRYSTAL STRUCTURE OF HUMANIZED XENOPUS MDM2 WITH NUTLIN-3A
 
Authors :  B. J. Graves, C. M. Lukacs, R. U. Kammlott, R. Crowther
Date :  05 Feb 13  (Deposition) - 24 Apr 13  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A
Keywords :  Mdm2, Protein-Protein Interaction, Imidazoline, Ligase-Antagonist Complex, E3 Ubiquitin Ligase, P53, Nucleus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Vu, P. Wovkulich, G. Pizzolato, A. Lovey, Q. Ding, N. Jiang, J. J. Liu C. Zhao, K. Glenn, Y. Wen, C. Tovar, K. Packman, L. Vassilev, B. Graves
Discovery Of Rg7112: A Small-Molecule Mdm2 Inhibitor In Clinical Development.
Acs Med Chem Lett V. 4 466 2013
PubMed-ID: 24900694  |  Reference-DOI: 10.1021/ML4000657
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUBS 520
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (UNP RESIDUES 21-105)
    Gene: MDM2
    Mutation: YES
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: DOUBLE MINUTE 2 PROTEIN, XDM2, P53-BINDING PROTEIN MDM2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NUT1Ligand/Ion4-({(4S,5R)-4,5-BIS(4-CHLOROPHENYL)-2-[4-METHOXY-2-(PROPAN-2-YLOXY)PHENYL]-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}CARBONYL)PIPERAZIN-2-ONE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:50 , LEU A:53 , GLY A:54 , GLN A:55 , ILE A:57 , MET A:58 , VAL A:89 , HIS A:92 , ILE A:95 , TYR A:96 , HOH A:306 , HOH A:308 , HOH A:347BINDING SITE FOR RESIDUE NUT A 201
2AC2SOFTWAREMET A:20 , ASN A:75 , GLU A:91 , HIS A:92 , ARG A:93 , ARG A:94 , HOH A:311 , HOH A:335 , HOH A:341 , HOH A:388BINDING SITE FOR RESIDUE SO4 A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J3E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J3E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J3E)

(-) Exons   (0, 0)

(no "Exon" information available for 4J3E)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:86
                                                                                                                      
               SCOP domains d4j3ea_ A: MDM2                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........eee....hhhhhhh..eee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4j3e A  20 MEKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLVS 105
                                    29        39        49        59        69        79        89        99
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J3E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J3E)

(-) Gene Ontology  (11, 11)

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
        MDM2_XENLA | P56273: 1ttv 1ycq 4ipf 4j74 4j7d 4j7e 4jrg 4jsc 4lwt 4lwu 4lwv

(-) Related Entries Specified in the PDB File

1rv1 HUMAN MDM2 COMPLEXED WITH NUTLIN-2
4ipf SAME PROTEIN COMPLEXED WITH RO5045337