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

(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE TRANSCRIPTIONAL REGULATOR SLYA
 
Authors :  R. Y. Wu, R. G. Zhang, P. Gornicki, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  19 Apr 02  (Deposition) - 21 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hth Dna Binding Protein, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Y. Wu, R. G. Zhang, O. Zagnitko, I. Dementieva, N. Maltzev, J. D. Watson, R. Laskowski, P. Gornicki, A. Joachimiak
Crystal Structure Of Enterococcus Faecalis Slya-Like Transcriptional Factor
J. Biol. Chem. V. 278 20240 2003
PubMed-ID: 12649270  |  Reference-DOI: 10.1074/JBC.M300292200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR SLYA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEX1
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneREF02436
    Organism ScientificENTEROCOCCUS FAECALIS
    Organism Taxid1351

 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 1LJ9)

(-) Sites  (0, 0)

(no "Site" information available for 1LJ9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LJ9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LJ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LJ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LJ9)

(-) Exons   (0, 0)

(no "Exon" information available for 1LJ9)

(-) 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:144
 aligned with Q82ZP8_ENTFA | Q82ZP8 from UniProtKB/TrEMBL  Length:150

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
         Q82ZP8_ENTFA     2 TDILREIGMIARALDSISNIEFKELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVKKG 145
               SCOP domains d1lj9a_ A: Transcriptional regulator SlyA                                                                                                        SCOP domains
               CATH domains 1lj9A00 A:2-145 'winged helix' repressor DNA binding domain                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lj9 A   2 TDILREIGMIARALDSISNIEFKELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVKKG 145
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with Q82ZP8_ENTFA | Q82ZP8 from UniProtKB/TrEMBL  Length:150

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
         Q82ZP8_ENTFA     2 TDILREIGMIARALDSISNIEFKELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVK 143
               SCOP domains d1lj9b_ B: Transcriptional regulator SlyA                                                                                                      SCOP domains
               CATH domains 1lj9B00 B:2-143 'winged helix' repressor DNA binding domain                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lj9 B   2 TDILREIGMIARALDSISNIEFKELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVK 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LJ9)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q82ZP8_ENTFA | Q82ZP8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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 1lj9)
 
  Sites
(no "Sites" information available for 1lj9)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1lj9)
 

(-) 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
  1lj9
    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
  Q82ZP8_ENTFA | Q82ZP8
    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
  Q82ZP8_ENTFA | Q82ZP8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1LJ9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LJ9)