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

(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR VANUG, FORM I
 
Authors :  P. J. Stogios, E. Evdokimova, Z. Wawrzak, A. Dong, F. Depardieu, P. Cour I. Shabalin, M. Chruszcz, W. Minor, A. Savchenko, W. F. Anderson, Cent Structural Genomics Of Infectious Diseases (Csgid)
Date :  26 Sep 11  (Deposition) - 12 Oct 11  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Helix-Turn-Helix, Transcription Regulator, Vancomycin Resistance, Vang Phenotype, Dna, Cytoplasmic, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Stogios, E. Evdokimova, Z. Wawrzak, A. Dong, F. Depardieu, P. Courvalin, I. Shabalin, M. Chruszcz, W. Minor, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Transcriptional Regulator Vanug, Form
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-67
    Gene: VANU, VANUG
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Strain: BM4518
    Synonym: VANU

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3TYR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TYR)

(-) 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:75
 aligned with Q6WRY9_ENTFL | Q6WRY9 from UniProtKB/TrEMBL  Length:75

    Alignment length:75
                                    1                                                                  
                                    |2        12        22        32        42        52        62     
          Q6WRY9_ENTFL    - --------MRVSYNKLWKLLIDRDMKKGELREAVGVSKSTFAKLGKNENVSLTVLLAICEYLNCDFGDIIEALPE 67
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhh.hhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  3tyr A 14 RENLYFQGmRVSYNKLWKLLIDRDmKKGELREAVGVSKSTFAKLGKNENVSLTVLLAICEYLNCDFGDIIEALPE 88
                                    23        33    |   43        53        63        73        83     
                                   22-MSE          38-MSE                                              


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with Q6WRY9_ENTFL | Q6WRY9 from UniProtKB/TrEMBL  Length:75

    Alignment length:74
                                   1                                                                  
                                   | 3        13        23        33        43        53        63    
          Q6WRY9_ENTFL    - -------MRVSYNKLWKLLIDRDMKKGELREAVGVSKSTFAKLGKNENVSLTVLLAICEYLNCDFGDIIEALPE 67
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeehhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhh.hhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  3tyr B 15 ENLYFQGmRVSYNKLWKLLIDRDmKKGELREAVGVSKSTFAKLGKNENVSLTVLLAICEYLNCDFGDIIEALPE 88
                                   |24        34   |    44        54        64        74        84    
                                  22-MSE          38-MSE
   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 3TYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6WRY9_ENTFL | Q6WRY9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3tyr)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3tyr)
 

(-) 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 ](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
  3tyr
    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
  Q6WRY9_ENTFL | Q6WRY9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q6WRY9_ENTFL | Q6WRY9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q6WRY9_ENTFL | Q6WRY9: 3tys

(-) Related Entries Specified in the PDB File

3tys CRYSTAL STRUCTURE OF TRANSCRIPTION REGULATOR VANUG, FORM II RELATED ID: IDP91041 RELATED DB: TARGETDB