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 S. AUREUS MEPR IN DNA-BINDING CONFORMATION
 
Authors :  I. Birukou, R. G. Brennan
Date :  18 Jun 13  (Deposition) - 11 Sep 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Winged Helix-Turn-Helix, Whth, Transcription Repressor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Birukou, N. K. Tonthat, S. M. Seo, B. D. Schindler, G. W. Kaatz, R. G. Brennan
The Molecular Mechanisms Of Allosteric Mutations Impairing Mepr Repressor Function In Multidrug-Resistant Strains Of Staphylococcus Aureus.
Mbio V. 4 00528 2013
PubMed-ID: 23982071  |  Reference-DOI: 10.1128/MBIO.00528-13

(-) Compounds

Molecule 1 - MEPR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Gene: MEPR
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: NCTC 8325-4
    Synonym: MARR FAMILY TRANSCRIPTION REPRESSOR MEPR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4L9J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L9J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu B:57 -Gln B:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L9J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L9J)

(-) Exons   (0, 0)

(no "Exon" information available for 4L9J)

(-) 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.........eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l9j A   2 EFTYSYLFRmISHEmKQKADQKLEQFDITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEAFTSIFDEmEQTLVSQLSEEENEQmKANLTKmLSSLQ 139
                                    11    |   21        31        41        51        61        71        81        91       101       111       121     | 131  |     
                                    11-MSE|                                                                                            111-MSE         127-MSE  |     
                                         16-MSE                                                                                                               134-MSE 


Chain B from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9j B   3 FTYSYLFRmISHEmKQKADQKLEQFDITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEAFTSIFDEmEQTLVSQLSEEENEQmKANLTKmLSSLQ 139
                                    12   |    22        32        42        52        62        72        82        92       102       112       122    |  132 |     
                                   11-MSE|                                                                                            111-MSE         127-MSE  |     
                                        16-MSE                                                                                                               134-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 4L9J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L9J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L9J)

(-) 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4l9j)
 
  Cis Peptide Bonds
    Leu B:57 - Gln B:58   [ 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 ](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
  4l9j
    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
  Q5Y812_STAAU | Q5Y812
    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
  Q5Y812_STAAU | Q5Y812
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q5Y812_STAAU | Q5Y812: 5f6f 5ffx
UniProtKB/TrEMBL
        Q5Y812_STAAU | Q5Y812: 4l9n 4l9t 4l9v 4ld5 4lll 4lln 5fb2 5ffz

(-) Related Entries Specified in the PDB File

4l9n 4l9t 4l9v 4ld5