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 THE N-TERMINUS Y153H BROMODOMAIN MUTANT OF HUMAN BRD2
 
Authors :  C. Tallant, C. Lori, A. Pasquo, R. Chiaraluce, V. Consalvi, J. A. Newman Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, S. Knapp
Date :  06 Jan 16  (Deposition) - 20 Jan 16  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription Regulation, Post Translational Modifications Recognition, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Tallant, C. Lori, A. Pasquo, R. Chiaraluce, V. Consalvi, J. A. Newman, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra S. Knapp
Crystal Structure Of The N-Terminus Y153H Bromodomain Mutan Of Human Brd2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 71-194
    Gene: BRD2, KIAA9001, RING3
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:110 , ASN A:156 , HOH A:305 , HOH A:389binding site for residue EDO A 201
2AC2SOFTWAREARG A:129 , GLU A:140 , GLN A:143 , ASP A:144 , HOH A:302 , HOH A:303 , HOH A:370binding site for residue EDO A 202
3AC3SOFTWAREGLN A:94 , TRP A:97 , PRO A:158 , HOH A:341 , HOH A:360 , HOH A:362binding site for residue EDO A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HEL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HEL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HEL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HEL)

(-) Exons   (0, 0)

(no "Exon" information available for 5HEL)

(-) 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:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh...hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5hel A  69 SMKPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCHIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQEL 187
                                    78        88        98       108       118       128       138       148       158       168       178
   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 5HEL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HEL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HEL)

(-) Gene Ontology  (10, 10)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5hel)
 

(-) 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
  5hel
    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
  BRD2_HUMAN | P25440
    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
  BRD2_HUMAN | P25440
    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
        BRD2_HUMAN | P25440: 1x0j 2dvq 2dvr 2dvs 2dvv 2e3k 2g4a 2ydw 2yek 3aqa 3oni 4a9e 4a9f 4a9h 4a9i 4a9j 4a9m 4a9n 4a9o 4akn 4alg 4alh 4j1p 4mr5 4mr6 4qeu 4qev 4qew 4uyf 4uyg 4uyh 5bt5 5dfb 5dfc 5dfd 5dw1 5ek9 5hem 5hen 5hfq 5ibn 5ig6 5u5s 5uew

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HEL)