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

(-) Description

Title :  CRYSTAL STRUCTURE OF TRIM24 PHD-BROMODOMAIN COMPLEXED WITH N-{1,3-DIMETHYL-6-[3-(2-METHYLPROPOXY)PHENOXY]-2-OXO-2,3-DIHYDRO-1H-1,3-BENZODIAZOL-5-YL}-1,2-DIMETHYL-1H-IMIDAZOLE-4-SULFONAMIDE (7G)
 
Authors :  G. Poncet-Montange, W. Palmer, P. Jones
Date :  19 Feb 15  (Deposition) - 24 Jun 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A
Keywords :  Center For Biomolecular Structure And Function, Bromodomain, Trim24, Inhibitor, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. S. Palmer, G. Poncet-Montange, G. Liu, A. Petrocchi, N. Reyna, G. Subramanian, J. Theroff, A. Yau, M. Kost-Alimova, J. P. Bardenhagen, E. Leo, H. E. Shepard, T. N. Tieu, X. Shi, Y. Zhan, S. Zhao, M. C. Barton, G. Draetta, C. Toniatti, P. Jones, M. Geck Do, J. N. Andersen
Structure-Guided Design Of Iacs-9571, A Selective High-Affinity Dual Trim24-Brpf1 Bromodomain Inhibitor.
J. Med. Chem. V. 59 1440 2016
PubMed-ID: 26061247  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00405

(-) Compounds

Molecule 1 - TRANSCRIPTION INTERMEDIARY FACTOR 1-ALPHA
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BROMODOMAIN (UNP RESIDUES 824-1006)
    Gene: TRIM24, RNF82, TIF1, TIF1A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TIF1-ALPHA,E3 UBIQUITIN-PROTEIN LIGASE TRIM24,RING FINGER PROTEIN 82,TRIPARTITE MOTIF-CONTAINING PROTEIN 24

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
14BK1Ligand/IonN-{1,3-DIMETHYL-6-[3-(2-METHYLPROPOXY)PHENOXY]-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL}-1,2-DIMETHYL-1H-IMIDAZOLE-4-SULFONAMIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:829 , CYS A:832 , HIS A:849 , CYS A:852binding site for residue ZN A 1101
2AC2SOFTWARECYS A:841 , CYS A:844 , CYS A:867 , CYS A:870binding site for residue ZN A 1102
3AC3SOFTWAREALA A:923 , PHE A:924 , VAL A:928 , PHE A:979 , ASN A:980 , GLU A:985 , ALA A:989 , HOH A:1266binding site for residue 4BK A 1103
4AC4SOFTWAREPRO A:902 , ARG A:906 , LYS A:1002 , HOH A:1236binding site for residue DMS A 1104

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:854 -Pro A:855

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YBS)

(-) 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    
   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:178
                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee......ee...............................hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ybs A  824 PNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   833       843       853       863       873       883 ||    898       908       918       928       938       948       958       968       978       988       998        
                                                                                       885|                                                                                                                   
                                                                                        891
   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  (0, 0)

(no "SCOP Domain" information available for 4YBS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    4BK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:854 - Pro A:855   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4ybs
    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
  TIF1A_HUMAN | O15164
    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)
  6.3.2.-
    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
  TIF1A_HUMAN | O15164
    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
        TIF1A_HUMAN | O15164: 2yyn 3o33 3o34 3o35 3o36 3o37 4yab 4yad 4yat 4yax 4ybm 4ybt 4yc9 4zql 5h1t 5h1u 5h1v

(-) Related Entries Specified in the PDB File

4yab 4yad 4yat 4yax 4ybm 4ybt 4yc9