Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF HDMX WITH DIMER INDUCING INDOLYL HYDANTOIN RO-2443
 
Authors :  C. M. Lukacs, C. A. Janson, B. J. Graves
Date :  29 Sep 11  (Deposition) - 27 Jun 12  (Release) - 01 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cell Cycle, Ubiquitin Ligase, Mdm2, Mdmx, P53, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Graves, T. Thompson, M. Xia, C. Janson, C. Lukacs, D. Deo, P. Di Lello, D. Fry, C. Garvie, K. S. Huang, L. Gao, C. Tovar, A. Lovey, J. Wanner, L. T. Vassilev
Activation Of The P53 Pathway By Small-Molecule-Induced Mdm And Mdmx Dimerization.
Proc. Natl. Acad. Sci. Usa V. 109 11788 2012
PubMed-ID: 22745160  |  Reference-DOI: 10.1073/PNAS.1203789109

(-) Compounds

Molecule 1 - PROTEIN MDM4
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 14-111
    Gene: MDM4, MDMX
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DOUBLE MINUTE 4 PROTEIN, MDM2-LIKE P53-BINDING PROTEIN, PROTEIN MDMX, P53-BINDING PROTEIN MDM4

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
103M4Ligand/Ion(5Z)-5-[(6-CHLORO-7-METHYL-1H-INDOL-3-YL)METHYLIDENE]-3-(3,4-DIFLUOROBENZYL)IMIDAZOLIDINE-2,4-DIONE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
103M2Ligand/Ion(5Z)-5-[(6-CHLORO-7-METHYL-1H-INDOL-3-YL)METHYLIDENE]-3-(3,4-DIFLUOROBENZYL)IMIDAZOLIDINE-2,4-DIONE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
103M2Ligand/Ion(5Z)-5-[(6-CHLORO-7-METHYL-1H-INDOL-3-YL)METHYLIDENE]-3-(3,4-DIFLUOROBENZYL)IMIDAZOLIDINE-2,4-DIONE
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:57 , ILE A:60 , MET A:61 , TYR A:66 , GLN A:71 , VAL A:92 , HOH A:118 , HOH A:121 , 03M B:1 , MET B:53 , GLY B:57 , ILE B:60 , PHE B:90 , VAL B:92 , LEU B:98BINDING SITE FOR RESIDUE 03M A 1
2AC2SOFTWAREGLN A:71 , HIS A:72 , LYS A:93 , GLU B:70 , GLN B:71 , HIS B:72 , LYS B:93BINDING SITE FOR RESIDUE SO4 A 112
3AC3SOFTWARE03M A:1 , MET A:53 , LEU A:56 , GLY A:57 , PHE A:90 , VAL A:92 , LEU A:98 , GLY B:57 , ILE B:60 , MET B:61 , TYR B:66 , GLN B:71BINDING SITE FOR RESIDUE 03M B 1
4AC4SOFTWAREILE C:60 , MET C:61 , TYR C:66 , GLN C:71 , VAL C:92 , HOH C:118 , HOH C:136 , 03M D:1 , MET D:53 , LEU D:56 , GLY D:57 , ILE D:60 , VAL D:92 , LEU D:98BINDING SITE FOR RESIDUE 03M C 1
5AC5SOFTWARE03M C:1 , MET C:53 , LEU C:56 , GLY C:57 , ILE C:60 , GLN C:71 , PHE C:90 , VAL C:92 , LEU C:98 , GLY D:57 , ILE D:60 , MET D:61 , TYR D:66 , GLN D:68 , GLN D:71 , HOH D:119 , HOH D:139BINDING SITE FOR RESIDUE 03M D 1
6AC6SOFTWAREGLN C:71 , HIS C:72 , GLU D:70 , GLN D:71 , HIS D:72BINDING SITE FOR RESIDUE SO4 D 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U15)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U15)

(-) Exons   (4, 16)

Asymmetric Unit (4, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003671821aENSE00001443738chr1:204485511-204485637127MDM4_HUMAN-00--
1.2aENST000003671822aENSE00002156140chr1:204494612-204494724113MDM4_HUMAN1-26264A:26-26
B:26-26
C:26-26
D:26-26		1
1
1
1
1.3ENST000003671823ENSE00001039934chr1:204495488-20449556275MDM4_HUMAN27-51254A:27-51
B:27-51
C:27-51
D:27-51		25
25
25
25
1.4ENST000003671824ENSE00001039926chr1:204499812-204499945134MDM4_HUMAN52-96454A:52-96
B:52-96
C:52-96
D:52-96		45
45
45
45
1.5aENST000003671825aENSE00001039924chr1:204501319-20450137456MDM4_HUMAN96-115204A:96-107
B:96-107
C:96-107
D:96-106		12
12
12
11
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:82
 aligned with MDM4_HUMAN | O15151 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:82
                                    35        45        55        65        75        85        95       105  
           MDM4_HUMAN    26 QVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLV 107
               SCOP domains d3u15a_ A: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhh........hhhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee...hhhhhhhhhhhee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 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)
                 3u15 A  26 QVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLV 107
                                    35        45        55        65        75        85        95       105  


Chain B from PDB  Type:PROTEIN  Length:82
 aligned with MDM4_HUMAN | O15151 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:82
                                    35        45        55        65        75        85        95       105  
           MDM4_HUMAN    26 QVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLV 107
               SCOP domains d3u15b_ B: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..............hhhhhhh.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 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)
                 3u15 B  26 QVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLV 107
                                    35        45        55        65        75        85        95       105  


Chain C from PDB  Type:PROTEIN  Length:82
 aligned with MDM4_HUMAN | O15151 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:82
                                    35        45        55        65        75        85        95       105  
           MDM4_HUMAN    26 QVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLV 107
               SCOP domains d3u15c_ C: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhhhh......hhhhhhhhhhhhhhhh..ee..eeeeee...hhhhhhhh..eee...hhhhhhhhh..ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 1.3  PDB: C:27-51   Exon 1.4  PDB: C:52-96 UniProt: 52-96        ----------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.5a    Transcript 1 (2)
                 3u15 C  26 QVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLV 107
                                    35        45        55        65        75        85        95       105  


Chain D from PDB  Type:PROTEIN  Length:81
 aligned with MDM4_HUMAN | O15151 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:81
                                    35        45        55        65        75        85        95       105 
           MDM4_HUMAN    26 QVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNL 106
               SCOP domains d3u15d_ D: automated matches                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.......hhhhhhhhhhhhhhhh.........eee.....hhhhhh..eee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 1.3  PDB: D:27-51   Exon 1.4  PDB: D:52-96 UniProt: 52-96        ---------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.5a   Transcript 1 (2)
                 3u15 D  26 QVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNL 106
                                    35        45        55        65        75        85        95       105
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U15)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U15)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    03M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3u15)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3u15
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MDM4_HUMAN | O15151
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MDM4_HUMAN | O15151
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MDM4_HUMAN | O15151: 2cr8 2mwy 2n06 2n0u 2n0w 2n14 2vje 2vjf 2vyr 3dab 3eqy 3fdo 3fe7 3fea 3jzo 3jzp 3jzq 3lbj 3mqr 4rxz 5mnj

(-) Related Entries Specified in the PDB File

3fea STARTING MODEL FOR MOLECULAR REPLACEMENT.
3vbg