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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF DEST IN COMPLEX WITH DUPLEX DNA
 
Authors :  D. J. Miller, S. W. White
Date :  12 Feb 10  (Deposition) - 04 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Transcriptional Repressor, Dest-Dna Complex, Tetr Family, Dna- Binding, Transcription, Transcription Regulation, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Miller, Y. M. Zhang, C. Subramanian, C. O. Rock, S. W. White
Structural Basis For The Transcriptional Regulation Of Membrane Lipid Homeostasis.
Nat. Struct. Mol. Biol. V. 17 971 2010
PubMed-ID: 20639888  |  Reference-DOI: 10.1038/NSMB.1847

(-) Compounds

Molecule 1 - DEST
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21DE3
    Expression System Taxid562
    GeneDEST, PA4890
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
 
Molecule 2 - DNA (27-MER)
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:14 , SER A:18 , ARG A:21 , HIS A:22 , SER A:105 , HOH A:230BINDING SITE FOR RESIDUE SO4 A 221
2AC2SOFTWAREGLY A:87 , LEU A:88 , ILE A:89 , ARG A:195 , HOH A:233 , HOH A:234BINDING SITE FOR RESIDUE SO4 A 222

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LSR)

(-) 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:192
 aligned with Q9HUS3_PSEAE | Q9HUS3 from UniProtKB/TrEMBL  Length:209

    Alignment length:202
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  
         Q9HUS3_PSEAE     4 PRAEQKQQTRHALMSAARHLMESGRGFGSLSLREVTRAAGIVPAGFYRHFSDMDQLGLALVAEVDETFRATLRAVRRNEFELGGLIDASVRIFLDAVGANRSQFLFLAREQYGGSLPIRQAIASLRQRITDDLAADLALLNKMPHLDGAALDVFADLVVKTVFATLPELIDPPAADLPPHLMPAAKITHQLRFIMIGGKHWH 205
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------TetR_N-3lsrA01 A:16-63                          ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.----------hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lsr A   4 PRAEQKQQTRHALMSAARHLMESGRGFGSLSLREVTRAAGIVPAGFYRHFSDMDQLGLALVAEVDETFRATLRAVRRNEFELGGLIDASVRIFLDAVGANRSQFLFLAREQYGGSLPIRQAIASLRQRITDDLAADLALLNKMPHLDGAALDVFADLVVKTVFATLPELIDP----------PAAKITHQLRFIMIGGKHWH 205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173 |       -  |    193       203  
                                                                                                                                                                                                     175        186                   

Chain B from PDB  Type:DNA  Length:27
                                                           
                 3lsr B   4 CATCAGTGAACGCGCGTTCACTGATGT  30
                                    13        23       

   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 3LSR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9HUS3_PSEAE | Q9HUS3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0045922    negative regulation of fatty acid metabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving fatty acids.
    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.

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lsr)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3lsr
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9HUS3_PSEAE | Q9HUS3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q9HUS3_PSEAE | Q9HUS3
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9HUS3_PSEAE | Q9HUS33lsj 3lsp

(-) Related Entries Specified in the PDB File

3lsj SAME PROTEIN WITHOUT DNA
3lsp PSEDOPALINDROME DNA BOUND TO DEST