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(-) Description

Title :  THE 1.25A CRYSTAL STRUCTURE OF HUMANIZED XENOPUS MDM2 WITH A NUTLIN FRAGMENT, RO5045331
 
Authors :  C. Janson, C. Lukacs, B. Graves
Date :  13 Feb 13  (Deposition) - 07 Aug 13  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Protein Interaction, E3 Ubiquitin Ligase, Ligase-Antagonist Complex, P53, Imidazoline, Nucleus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Fry, C. Wartchow, B. Graves, C. Janson, C. Lukacs, U. Kammlott, C. Belunis, S. Palme, C. Klein, B. Vu
Deconstruction Of A Nutlin: Dissecting The Binding Determinants Of A Potent Protein-Protein Interaction Inhibitor.
Acs Med Chem Lett V. 4 660 2013
PubMed-ID: 24900726  |  Reference-DOI: 10.1021/ML400062C
(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, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1I311Ligand/Ion(4S,5R)-2-(4-TERT-BUTYL-2-ETHOXYPHENYL)-4,5-BIS(4-CHLOROPHENYL)-4,5-DIMETHYL-4,5-DIHYDRO-1H-IMIDAZOLE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:36 , LEU A:50 , MET A:58 , ALA A:59 , LYS A:60 , GLN A:61 , HIS A:69 , VAL A:89 , HIS A:92 , TYR A:96 , HOH A:302 , HOH A:309BINDING SITE FOR RESIDUE I31 A 201
2AC2SOFTWAREPRO A:28 , LEU A:29 , ARG A:93 , ARG A:94 , HOH A:365BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWARELYS A:41 , GLU A:42 , THR A:43 , HIS A:69 , SER A:88 , HOH A:328 , HOH A:359 , HOH A:383BINDING SITE FOR RESIDUE SO4 A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J7D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J7D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J7D)

(-) Exons   (0, 0)

(no "Exon" information available for 4J7D)

(-) 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    
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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 d4j7da_ A: MDM2                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhhhhhhhh......eehhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4j7d 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 4J7D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J7D)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  4j7d
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  MDM2_XENLA | P56273
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4ipf SAME PROTEIN WITH RG7112
4j3e SAME PROTEIN WITH NUTLIN-3
4j74 SAME PROTEIN WITH A DIFFERENT FRAGMENT - RO0503918
4j7e