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 HUMAN BAZ2B IN COMPLEX WITH FRAGMENT-4 N09496
 
Authors :  A. R. Bradley, Y. Liu, T. Krojer, C. Bountra, C. H. Arrowsmith, A. Edward S. Knapp, F. Von Delft
Date :  21 Mar 14  (Deposition) - 02 Apr 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R Bradley, Y. Liu, T. Krojer, C. Bountra, C. H. Arrowsmith, A. Edwards, S. Knapp, F. Von Delft
Crystal Structure Of Human Baz2B In Complex With Fragment-4 N09496
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3
    Expression System Vector Type: PLASMID
    Fragment: BROMODOMAIN, RESIDUES 1858-1972
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HWALP4, BAZ2B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2ES11Ligand/IonQUINOLIN-4-OL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:1879 , THR A:1968 , HOH A:2124BINDING SITE FOR RESIDUE EDO A2971
2AC2SOFTWAREPRO A:1888 , ASN A:1944 , HOH A:2056 , HOH A:2127BINDING SITE FOR RESIDUE ES1 A2972
3AC3SOFTWARELYS A:1896 , LYS A:1902 , GLU A:1945BINDING SITE FOR RESIDUE EDO A2973
4AC4SOFTWAREHIS A:1883 , GLU A:1884BINDING SITE FOR RESIDUE EDO A2974
5AC5SOFTWARELEU A:1895 , LYS A:1896 , PRO A:1899BINDING SITE FOR RESIDUE EDO A2975
6AC6SOFTWAREARG A:1864 , LEU A:1872 , THR A:1968BINDING SITE FOR RESIDUE EDO A2976

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CUS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.BAZ2B_HUMAN2077-2147  1A:1881-1951
2BROMODOMAIN_1PS00633 Bromodomain signature.BAZ2B_HUMAN2082-2139  1A:1886-1943

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003927831aENSE00001893988chr2:160473203-160472753451BAZ2B_HUMAN-00--
1.3aENST000003927833aENSE00001386868chr2:160412376-16041233443BAZ2B_HUMAN-00--
1.5ENST000003927835ENSE00002146728chr2:160335232-160335086147BAZ2B_HUMAN1-49490--
1.7ENST000003927837ENSE00001740643chr2:160310312-160310124189BAZ2B_HUMAN49-112640--
1.8bENST000003927838bENSE00001680744chr2:160304920-160304753168BAZ2B_HUMAN112-168570--
1.9ENST000003927839ENSE00001656854chr2:160303486-160303293194BAZ2B_HUMAN168-232650--
1.10aENST0000039278310aENSE00001009654chr2:160295723-160295520204BAZ2B_HUMAN233-300680--
1.10cENST0000039278310cENSE00000840721chr2:160295206-160294814393BAZ2B_HUMAN301-4311310--
1.11bENST0000039278311bENSE00000840720chr2:160289874-160289268607BAZ2B_HUMAN432-6342030--
1.12ENST0000039278312ENSE00000840719chr2:160287667-160287374294BAZ2B_HUMAN634-732990--
1.13ENST0000039278313ENSE00000840718chr2:160285771-16028571161BAZ2B_HUMAN732-752210--
1.14ENST0000039278314ENSE00000840717chr2:160284930-160284822109BAZ2B_HUMAN752-788370--
1.15ENST0000039278315ENSE00000840716chr2:160284553-160284452102BAZ2B_HUMAN789-822340--
1.17bENST0000039278317bENSE00000840715chr2:160269056-160268846211BAZ2B_HUMAN823-893710--
1.18ENST0000039278318ENSE00000840714chr2:160261625-16026153393BAZ2B_HUMAN893-924320--
1.19aENST0000039278319aENSE00001173508chr2:160261421-16026136062BAZ2B_HUMAN924-944210--
1.20aENST0000039278320aENSE00000840712chr2:160257175-16025711066BAZ2B_HUMAN945-966220--
1.21ENST0000039278321ENSE00000840711chr2:160255405-16025534066BAZ2B_HUMAN967-988220--
1.22ENST0000039278322ENSE00000840710chr2:160253900-16025385645BAZ2B_HUMAN989-1003150--
1.24ENST0000039278324ENSE00000840709chr2:160252345-16025228066BAZ2B_HUMAN1004-1025220--
1.26ENST0000039278326ENSE00000840708chr2:160245996-160245856141BAZ2B_HUMAN1026-1072470--
1.27bENST0000039278327bENSE00000840707chr2:160243118-160242864255BAZ2B_HUMAN1073-1157850--
1.28bENST0000039278328bENSE00000840706chr2:160241880-160241666215BAZ2B_HUMAN1158-1229720--
1.29ENST0000039278329ENSE00001173601chr2:160240191-16024011775BAZ2B_HUMAN1229-1254260--
1.30ENST0000039278330ENSE00001173595chr2:160239313-160239070244BAZ2B_HUMAN1254-1335820--
1.31ENST0000039278331ENSE00000840703chr2:160231264-16023120263BAZ2B_HUMAN1336-1356210--
1.32ENST0000039278332ENSE00001148127chr2:160229700-160229556145BAZ2B_HUMAN1357-1405490--
1.33ENST0000039278333ENSE00001173562chr2:160206868-160206219650BAZ2B_HUMAN1405-16212170--
1.34ENST0000039278334ENSE00000840700chr2:160205791-160205518274BAZ2B_HUMAN1622-1713920--
1.35ENST0000039278335ENSE00001173555chr2:160205344-160205189156BAZ2B_HUMAN1713-1765530--
1.36aENST0000039278336aENSE00001173549chr2:160204157-160203997161BAZ2B_HUMAN1765-1818540--
1.37aENST0000039278337aENSE00000840697chr2:160194283-160194078206BAZ2B_HUMAN1819-1887690--
1.38bENST0000039278338bENSE00001173542chr2:160193588-160193453136BAZ2B_HUMAN1887-1932460--
1.39ENST0000039278339ENSE00000840695chr2:160189197-160189051147BAZ2B_HUMAN1933-1981490--
1.40bENST0000039278340bENSE00000840694chr2:160182429-160182164266BAZ2B_HUMAN1982-2070891A:1856-1874 (gaps)24
1.41ENST0000039278341ENSE00001173525chr2:160181465-160181322144BAZ2B_HUMAN2070-2118491A:1874-192249
1.42ENST0000039278342ENSE00001148115chr2:160176929-1601754901440BAZ2B_HUMAN2118-2168511A:1922-197049

(-) 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:115
 aligned with BAZ2B_HUMAN | Q9UIF8 from UniProtKB/Swiss-Prot  Length:2168

    Alignment length:120
                                  2056      2066      2076      2086      2096      2106      2116      2126      2136      2146      2156      2166
         BAZ2B_HUMAN   2047 SKQESFTSVKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTFK 2166
               SCOP domains d     4cusa_ A: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .-----...........hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------------BROMODOMAIN_2  PDB: A:1881-1951 UniProt: 2077-2147                     ------------------- PROSITE (1)
                PROSITE (2) -----------------------------------BROMODOMAIN_1  PDB: A:1886-1943 UniProt: 2082-2139        --------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.40b [INCOMPLETE] -----------------------------------------------Exon 1.42  PDB: A:1922-1970 UniProt: 2118-2168    Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.41  PDB: A:1874-1922 UniProt: 2070-2118   ------------------------------------------------ Transcript 1 (2)
                4cus A 1856 S-----MSVKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTFK 1970
                            |     1860      1870      1880      1890      1900      1910      1920      1930      1940      1950      1960      1970
                            |  1857                                                                                                                 
                         1856
   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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BAZ2B_HUMAN | Q9UIF8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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/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 ]
    ES1  [ 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 4cus)
 

(-) 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
  4cus
    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
  BAZ2B_HUMAN | Q9UIF8
    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
  BAZ2B_HUMAN | Q9UIF8
    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
        BAZ2B_HUMAN | Q9UIF8: 2e7o 3g0l 3q2f 4cup 4cuq 4cur 4cut 4cuu 4ir3 4ir4 4ir5 4ir6 4nr9 4nra 4nrb 4nrc 4qc1 4qc3 4qf3 4rvr 4xua 4xub 5cq3 5cq4 5cq5 5cq6 5cq7 5cq8 5cqa 5cu8 5cua 5cub 5cuc 5cud 5cue 5cug 5dyu 5dyx 5e73 5e74 5e9i 5e9k 5e9l 5e9m 5e9y 5l8t 5l8u 5l96 5l97 5l98 5l99 5mge 5mgf 5mgg 5pb7 5pb8 5pb9 5pba 5pbb 5pbc 5pbd 5pbe 5pbf 5pbg 5pbh 5pbi 5pbj 5pbk 5pbl 5pbm 5pbn 5pbo 5pbp 5pbq 5pbr 5pbs 5pbt 5pbu 5pbv 5pbw 5pbx 5pby 5pbz 5pc0 5pc1 5pc2 5pc3 5pc4 5pc5 5pc6 5pc7 5pc8 5pc9 5pca 5pcb 5pcc 5pcd 5pce 5pcf 5pcg 5pch 5pci 5pcj 5pck 5pcl 5pcm 5pcn 5pco 5pcp 5pcq 5pcr 5pcs 5pct 5pcu 5pcv 5pcw 5pcx 5pcz 5pd0 5pd1 5pd2 5pd3 5pd4 5pd5 5pd6 5pd7 5pd8 5pd9 5pda 5pdb 5pdc 5pdd 5pde 5pdf 5pdg 5pdh 5pdi 5pdj 5pdk 5pdl 5pdm 5pdn 5pdo 5pdp 5pdq 5pdr 5pds 5pdt 5pdu 5pdv 5pdw 5pdx 5pdy 5pdz 5pe0 5pe1 5pe2 5pe3 5pe4 5pe5 5pe6 5pe7 5pe8 5pe9 5pea 5peb 5pec 5ped 5pee 5pef 5peg 5peh 5pei 5pej 5pek 5pel 5pem 5pen 5peo 5peq 5per 5pes 5pet 5peu 5pev 5pew 5pex 5pey 5pez 5pf0 5pf1 5pf2 5pf3 5pf4 5pf5 5pf6 5pf7 5pf8 5pf9 5pfa 5pfb 5pfc 5pfd 5pfe 5pff 5pfg 5pfh 5pfi 5pfj 5pfl 5pfm 5pfn 5pfo 5pfp 5pfq 5pfr 5pfs 5pft 5pfu 5pfv 5pfw 5pfx 5pfy 5pfz 5pg0 5pg1 5pg2 5pg3 5pg4 5pg5 5pg6 5pg7 5pg8 5pg9 5pga 5pgb 5pgc 5pgd 5pge 5pgf 5pgg 5pgh 5pgi 5pgj 5pgk 5pgl 5pgn 5pgo 5pgp 5pgq 5pgr 5pgs 5pgt

(-) Related Entries Specified in the PDB File

4cup CRYSTAL STRUCTURE OF HUMAN BAZ2B IN COMPLEX WITH FRAGMENT-1 N09421
4cuq CRYSTAL STRUCTURE OF HUMAN BAZ2B IN COMPLEX WITH FRAGMENT-2 N09594
4cur CRYSTAL STRUCTURE OF HUMAN BAZ2B IN COMPLEX WITH FRAGMENT-3 N09555
4cut CRYSTAL STRUCTURE OF HUMAN BAZ2B IN COMPLEX WITH FRAGMENT-5 N09428
4cuu CRYSTAL STRUCTURE OF HUMAN BAZ2B IN COMPLEX WITH FRAGMENT-6 N09645