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(-) Description

Title :  HUMAN MDMX LIGANDED WITH A 12MER PEPTIDE INHIBITOR (PDIQ)
 
Authors :  E. Schonbrunn, J. Phan
Date :  24 Sep 09  (Deposition) - 10 Nov 09  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,P,Q
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,Q  (1x)
Keywords :  Cell Cycle, P53-Binding Protein Mdm4, Double Minute 4 Protein, Alternative Splicing, Metal-Binding, Nucleus, Polymorphism, Zinc, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Phan, Z. Li, A. Kasprzak, B. Li, S. Sebti, W. Guida, E. Schonbrunn, J. Chen
Structure-Based Design Of High Affinity Peptides Inhibiting The Interaction Of P53 With Mdm2 And Mdmx.
J. Biol. Chem. V. 285 2174 2010
PubMed-ID: 19910468  |  Reference-DOI: 10.1074/JBC.M109.073056
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN MDM4
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST-HIS-MBP
    Expression System StrainBL21-GOLD (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMDM4, MDMX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP53-BINDING PROTEIN MDM4, MDM2-LIKE P53-BINDING PROTEIN, PROTEIN MDMX, DOUBLE MINUTE 4 PROTEIN
 
Molecule 2 - PDIQ PEPTIDE (12MER)
    ChainsP, Q
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABPQ
Biological Unit 1 (1x)A P 
Biological Unit 2 (1x) B Q

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:103 , HOH A:122 , GLU B:70 , GLN B:71 , HIS B:72 , GLU Q:1 , TRP Q:6BINDING SITE FOR RESIDUE SO4 B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JZQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JZQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JZQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JZQ)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003671821aENSE00001443738chr1:204485511-204485637127MDM4_HUMAN-00--
1.2aENST000003671822aENSE00002156140chr1:204494612-204494724113MDM4_HUMAN1-26262A:25-26
B:25-26
2
2
1.3ENST000003671823ENSE00001039934chr1:204495488-20449556275MDM4_HUMAN27-51252A:27-51
B:27-51
25
25
1.4ENST000003671824ENSE00001039926chr1:204499812-204499945134MDM4_HUMAN52-96452A:52-96
B:52-96
45
45
1.5aENST000003671825aENSE00001039924chr1:204501319-20450137456MDM4_HUMAN96-115202A:96-108
B:96-111
13
16
1.8aENST000003671828aENSE00001039927chr1:204506558-20450662568MDM4_HUMAN115-137230--
1.9dENST000003671829dENSE00001039922chr1:204507337-204507436100MDM4_HUMAN138-171340--
1.10bENST0000036718210bENSE00001075004chr1:204511912-204512072161MDM4_HUMAN171-224540--
1.11bENST0000036718211bENSE00001074998chr1:204513663-204513812150MDM4_HUMAN225-274500--
1.12bENST0000036718212bENSE00001075005chr1:204515925-20451600581MDM4_HUMAN275-301270--
1.13eENST0000036718213eENSE00001123001chr1:204518241-2045272489008MDM4_HUMAN302-4901890--

(-) Sequences/Alignments

Asymmetric 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:84
 aligned with MDM4_HUMAN | O15151 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:84
                                    34        44        54        64        74        84        94       104    
           MDM4_HUMAN    25 NQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVT 108
               SCOP domains d3jzqa_ A: automated matches                                                         SCOP domains
               CATH domains 3jzqA00 A:25-108 MDM2                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eehhhhhhhhhhh.......hhhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee...hhhhhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.Exon 1.3  PDB: A:27-51   Exon 1.4  PDB: A:52-96 UniProt: 52-96        ------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5a     Transcript 1 (2)
                 3jzq A  25 NQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVT 108
                                    34        44        54        64        74        84        94       104    

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with MDM4_HUMAN | O15151 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:87
                                    34        44        54        64        74        84        94       104       
           MDM4_HUMAN    25 NQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLAT 111
               SCOP domains d3jzqb_ B: automated matches                                                            SCOP domains
               CATH domains 3jzqB00 B:25-111 MDM2                                                                   CATH domains
           Pfam domains (1) -SWIB-3jzqB01 B:26-101                                                       ---------- Pfam domains (1)
           Pfam domains (2) -SWIB-3jzqB02 B:26-101                                                       ---------- Pfam domains (2)
         Sec.struct. author ...eehhhhhhhhhhh.......hhhhhhhhhhhhhhhh..ee..eeeeee...hhhhhhhh..eee...hhhhhhhhhhhee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.Exon 1.3  PDB: B:27-51   Exon 1.4  PDB: B:52-96 UniProt: 52-96        --------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5a        Transcript 1 (2)
                 3jzq B  25 NQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLAT 111
                                    34        44        54        64        74        84        94       104       

Chain P from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 3jzq P   1 ETFEHWWSQLLS  12
                                    10  

Chain Q from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 3jzq Q   1 ETFEHWWSQLLS  12
                                    10  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: SWIB (22)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MDM4_HUMAN | O15151)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030330    DNA damage response, signal transduction by p53 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0045023    G0 to G1 transition    The mitotic cell cycle phase transition whose occurrence commits the cell from the G0 quiescent state to the G1 phase. Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells. Appropriate stimulation of such cells induces them to return to G1 and resume growth and division. The G0 to G1 transition is accompanied by many changes in the program of gene expression.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    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:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042177    negative regulation of protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    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:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
cellular component
    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
        MDM4_HUMAN | O151512cr8 2mwy 2n06 2n0u 2n0w 2n14 2vje 2vjf 2vyr 3dab 3eqy 3fdo 3fe7 3fea 3jzo 3jzp 3lbj 3mqr 3u15 4rxz 5mnj

(-) Related Entries Specified in the PDB File

3jzo MDMX LIGANDED WITH PDI
3jzp MDMX LIGANDED WITH PDI6W
3jzr
3jzs