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 :  STRUCTURE OF PSEUDOMONAS AERUGINOSA TRANSCRIPTIONAL REGULATOR PA2196
 
Authors :  J. Choe, Y. Kang
Date :  31 Mar 11  (Deposition) - 04 Apr 12  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcriptional Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Choe, Y. Kang
Structure Of Pseudomonas Aeruginosa Transcriptional Regulator Pa2196
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PA2196
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3RD3)

(-) Sites  (0, 0)

(no "Site" information available for 3RD3)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:97 -A:100
2B:97 -B:100

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RD3)

(-) Exons   (0, 0)

(no "Exon" information available for 3RD3)

(-) 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:187
 aligned with Q9I1S1_PSEAE | Q9I1S1 from UniProtKB/TrEMBL  Length:194

    Alignment length:187
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       
         Q9I1S1_PSEAE     7 DTRQHLLDTGYRIMAVKGFSGVGLNEILQSAGVPKGSFYHYFKSKEQFGQALLEDYFRVYLADMDQRFSAPGLNARERLMSYWQKWLDNACPPCDEQRCLVVKLSAEVADLSESMRITLRDGSDGIIERLVGCLGQGRDDGSLAPCDARHMASALYQLWLGASLLSKLHRSPGPLETAMQTTRSLLE 193
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rd3 A   7 DTRQHLLDTGYRIMAVKGFSGVGLNEILQSAGVPKGSFYHYFKSKEQFGQALLEDYFRVYLADMDQRFSAPGLNARERLMSYWQKWLDNACPPCDEQRCLVVKLSAEVADLSESMRITLRDGSDGIIERLVGCLGQGRDDGSLAPCDARHMASALYQLWLGASLLSKLHRSPGPLETAMQTTRSLLE 193
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with Q9I1S1_PSEAE | Q9I1S1 from UniProtKB/TrEMBL  Length:194

    Alignment length:187
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       
         Q9I1S1_PSEAE     7 DTRQHLLDTGYRIMAVKGFSGVGLNEILQSAGVPKGSFYHYFKSKEQFGQALLEDYFRVYLADMDQRFSAPGLNARERLMSYWQKWLDNACPPCDEQRCLVVKLSAEVADLSESMRITLRDGSDGIIERLVGCLGQGRDDGSLAPCDARHMASALYQLWLGASLLSKLHRSPGPLETAMQTTRSLLE 193
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rd3 B   7 DTRQHLLDTGYRIMAVKGFSGVGLNEILQSAGVPKGSFYHYFKSKEQFGQALLEDYFRVYLADMDQRFSAPGLNARERLMSYWQKWLDNACPPCDEQRCLVVKLSAEVADLSESMRITLRDGSDGIIERLVGCLGQGRDDGSLAPCDARHMASALYQLWLGASLLSKLHRSPGPLETAMQTTRSLLE 193
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
   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 3RD3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RD3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RD3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9I1S1_PSEAE | Q9I1S1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000976    transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
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.

 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
(no "Ligands, Modified Residues, Ions" information available for 3rd3)
 
  Sites
(no "Sites" information available for 3rd3)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rd3)
 

(-) 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
  3rd3
    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
  Q9I1S1_PSEAE | Q9I1S1
    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
  Q9I1S1_PSEAE | Q9I1S1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9I1S1_PSEAE | Q9I1S1: 4l62

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RD3)