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 :  STRUCTURES OF INACTIVE AND ACTIVATED DNTR PROVIDE CONCLUSIVE EVIDENCE FOR THE MECHANISM OF ACTION OF LYSR TRANSCRIPTION FACTORS
 
Authors :  M. Lerche, C. Dian, A. Round, R. Lonneborg, P. Brzezinski, G. A. Leonard
Date :  25 Aug 15  (Deposition) - 13 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Lysr-Type Transcription Regulators, Lttr, Transcription Factor, Helix-Turn-Helix, Dna Binding Protein, Rossmann-Like Fold, Autoinducing Mutant, H169T-Dntr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lerche, C. Dian, A. Round, R. Lonneborg, P. Brzezinski, G. A. Leonar
The Solution Configurations Of Inactive And Activated Dntr Have Implications For The Sliding Dimer Mechanism Of Lysr Transcription Factors.
Sci. Rep. V. 6 19988 2016
PubMed-ID: 26817994  |  Reference-DOI: 10.1038/SREP19988

(-) Compounds

Molecule 1 - LYSR-TYPE REGULATORY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15
    Expression System Taxid: 1007065
    Expression System Variant: PREP4
    Expression System Vector: PQE-60
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BURKHOLDERIA CEPACIA
    Organism Taxid: 292
    Strain: DNT
    Synonym: DNTR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SCN2Ligand/IonTHIOCYANATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:104BINDING SITE FOR RESIDUE SCN A1304
2AC2SOFTWARETHR B:104BINDING SITE FOR RESIDUE SCN B1301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AE4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:184 -Pro A:185
2Gly B:136 -Asn B:137
3Ser B:184 -Pro B:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AE4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AE4)

(-) Exons   (0, 0)

(no "Exon" information available for 5AE4)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee........hhhhhhhhh....eeeeee....hhhhhhhhh..eeeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ae4 A  89 SFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRTRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEARH 303
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeehhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeehhhhhhhhh...eeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ae4 B  88 DSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRTRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSE 300
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
   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 5AE4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AE4)

(-) Gene Ontology  (4, 4)

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
    SCN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly B:136 - Asn B:137   [ RasMol ]  
    Ser A:184 - Pro A:185   [ RasMol ]  
    Ser B:184 - Pro B:185   [ 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
  5ae4
    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
  Q7WT50_9BURK | Q7WT50
    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
  Q7WT50_9BURK | Q7WT50
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7WT50_9BURK | Q7WT50: 1utb 1uth 2y7k 2y7p 2y7r 2y7w 2y84 5ae5

(-) Related Entries Specified in the PDB File

5ae5 STRUCTURES OF INACTIVE AND ACTIVATED DNTR PROVIDE CONCLUSIVE EVIDENCE FOR THE MECHANISM OF ACTION OF LYSR TRANSCRIPTION FACTORS