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 :  CRYSTAL STRUCTURE OF THE FIFTH BROMODOMAIN OF HUMAN PB1 IN COMPLEX WITH 1-PROPYLISOCHROMENO[3,4-C]PYRAZOL-5(2H)-ONE) COMPOUND
 
Authors :  C. Tallant, V. Myrianthopoulos, N. Gaboriaud-Kolar, J. A. Newman, S. P F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, E. Mikros, S
Date :  24 Jan 16  (Deposition) - 12 Oct 16  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pbrm1, Brg1-Associated Factor 180, Transcription, Chromatin Remodeling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Myrianthopoulos, N. Gaboriaud-Kolar, C. Tallant, M. L. Hall, S. Grigoriou, P. M. Brownlee, O. Fedorov, C. Rogers, D. Heidenreich, M. Wanior, N. Drosos, N. Mexia, P. Savitsky, T. Bagratuni, E. Kastritis, E. Terpos, P. Filippakopoulos, S. Muller, A. L. Skaltsounis, J. A. Downs, S. Knapp, E. Mikros
Discovery And Optimization Of A Selective Ligand For The Switch/Sucrose Nonfermenting-Related Bromodomains Of Polybromo Protein-1 By The Use Of Virtual Screening And Hydration Analysis.
J. Med. Chem. V. 59 8787 2016
PubMed-ID: 27617704  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00355

(-) Compounds

Molecule 1 - PROTEIN POLYBROMO-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 613-734
    Gene: PBRM1, BAF180, PB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPB1,BRG1-ASSOCIATED FACTOR 180,BAF180,POLYBROMO-1D,PB1 FIFTH BROMODOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
164E2Ligand/Ion1-PROPYLISOCHROMENO[3,4-C]PYRAZOL-5(3H)-ONE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
164E1Ligand/Ion1-PROPYLISOCHROMENO[3,4-C]PYRAZOL-5(3H)-ONE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
164E1Ligand/Ion1-PROPYLISOCHROMENO[3,4-C]PYRAZOL-5(3H)-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:683 , PHE A:684 , LEU A:687 , TYR A:696 , MET A:704 , ASP A:705 , MET A:731 , ALA A:735 , TYR A:738 , ASN A:739 , ILE A:745 , HOH A:911 , HOH A:923 , EDO B:802binding site for residue 64E A 801
2AC2SOFTWAREARG A:686 , EDO A:803binding site for residue EDO A 802
3AC3SOFTWAREARG A:686 , EDO A:802 , ARG B:676binding site for residue EDO A 803
4AC4SOFTWARELEU A:693 , PRO A:694 , ASP A:695 , TYR A:738binding site for residue EDO A 804
5AC5SOFTWAREMET A:655 , ASN A:663 , GLU A:664binding site for residue EDO A 805
6AC6SOFTWAREPHE A:732 , ASN A:733 , CYS A:736 , ALA A:749 , LEU A:750 , HIS A:753binding site for residue SO4 A 806
7AC7SOFTWAREILE B:683 , PHE B:684 , LEU B:687 , TYR B:696 , MET B:704 , MET B:731 , ALA B:735 , TYR B:738 , ASN B:739 , ILE B:745 , HOH B:904 , HOH B:916binding site for residue 64E B 801
8AC8SOFTWARE64E A:801 , HOH A:918 , SER B:743 , LEU B:744 , HOH B:906binding site for residue EDO B 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HRW)

(-) 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:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......hhhhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5hrw A 654 YMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 763
                                   663       673       683       693       703       713       723       733       743       753       763


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5hrw B 655 MTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRD 762
                                   664       674       684       694       704       714       724       734       744       754
   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 5HRW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

 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
    64E  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5hrw)
 
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
  5hrw
    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
  PB1_HUMAN | Q86U86
    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
  PB1_HUMAN | Q86U86
    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
        PB1_HUMAN | Q86U86: 2ktb 3g0j 3hmf 3iu5 3iu6 3k2j 3ljw 3mb4 3tlp 4q0n 4q0o 4y03 5e7d 5fh6 5fh7 5fh8 5hrv 5hrx 5ii1 5ii2 5iid

(-) Related Entries Specified in the PDB File

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