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 :  STRUCTURE OF SMET, THE REPRESSOR OF THE STENOTROPHOMONAS MALTOPHILIA MULTIDRUG EFFLUX PUMP SMEDEF.
 
Authors :  M. J. Mate, A. Romero, A. Hernandez, J. L. Martinez
Date :  04 Dec 08  (Deposition) - 07 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibiotic Resistance, Multi-Drug Efflux Pump, Transcription Regulation, Transcriptional Repressor, Dna Binding, Tetr Family, Dna-Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hernandez, M. J. Mate, P. Sanchez, A. Romero, F. Rojo, J. L. Martinez
Structural And Functional Analysis Of Smet, The Repressor Of The Stenotrophomonas Maltophilia Multidrug Efflux Pump Smedef.
J. Biol. Chem. V. 284 14428 2009
PubMed-ID: 19324881  |  Reference-DOI: 10.1074/JBC.M809221200

(-) Compounds

Molecule 1 - REPRESSOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAHF1
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: STENOTROPHOMONAS MALTOPHILIA
    Organism Taxid: 40324
    Other Details: IN MONOMER B MOST OF THE N-TERMINAL DOMAIN IS MISSING
    Synonym: SMET

 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
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:154 , GLU B:155 , LYS B:203 , HOH B:2134BINDING SITE FOR RESIDUE SO4 B1217
2AC2SOFTWAREARG A:154 , GLU A:155 , LYS A:203BINDING SITE FOR RESIDUE SO4 A1218

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W53)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W53)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W53)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W53)

(-) Exons   (0, 0)

(no "Exon" information available for 2W53)

(-) 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:202
 aligned with Q8KLP4_STEMA | Q8KLP4 from UniProtKB/TrEMBL  Length:219

    Alignment length:211
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 
         Q8KLP4_STEMA     7 EDTQATREGILDAAEACFHEHGVARTTLEMIGARAGYTRGAVYWHFKNKSEVLAAIVERVHLPFMQELERTSTDQRDTPVHDLRAVMIHSFIELSEDERLRKTMEIMLRSDASANTRVLTEMQQAGFRDALDRMERALRRARDLGQLREGADPKIAARMQHATVLGVLHGAMVEPELMDLKRDGMLALDMTLAAYVKDGVFVPGTVPEPLP 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.---------hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w53 A   7 EDTQATREGILDAAEACFHEHGVARTTLEMIGARAGYTRGAVYWHFKNKSEVLAAIVERVHLPFMQELERTSTDQRDTPVHDLRAVMIHSFIELSEDERLRKTMEIMLRS---------TEMQQAGFRDALDRMERALRRARDLGQLREGADPKIAARMLHATVLGVLHGAMVEPELMDLKRDGMLALDMTLAAYVKDGVFVPGTVPEPLP 217
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 
                                                                                                                                       116       126                                                                                           


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q8KLP4_STEMA | Q8KLP4 from UniProtKB/TrEMBL  Length:219

    Alignment length:204
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
         Q8KLP4_STEMA    13 REGILDAAEACFHEHGVARTTLEMIGARAGYTRGAVYWHFKNKSEVLAAIVERVHLPFMQELERTSTDQRDTPVHDLRAVMIHSFIELSEDERLRKTMEIMLRSDASANTRVLTEMQQAGFRDALDRMERALRRARDLGQLREGADPKIAARMQHATVLGVLHGAMVEPELMDLKRDGMLALDMTLAAYVKDGVFVPGTVPEPL 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---TetR_              N-2w53B01            B:16-62---------------------TetR_C_2-2w53B03 B:84-203                                                                                               ------------- Pfam domains (1)
           Pfam domains (2) ---TetR_              N-2w53B02            B:16-62---------------------TetR_C_2-2w53B04 B:84-203                                                                                               ------------- Pfam domains (2)
         Sec.struct. author hhhhhhhh--------------.hhhhhhh..-----------hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w53 B  13 REGILDAA--------------EMIGARAGYT-----------SEVLAAIVERVHLPFMQELERTSTDQRDTPVHDLRAVMIHSFIELSEDERLRKTMEIMLRS------RVLTEMQQAGFRDALDRMERALRRARDLGQLREGADPKIAARMLHATVLGVLHGAMVEPELMDLKRDGMLALDMTLAAYVKDGVFVPGTVPEPL 216
                                   | -         -  |     42 |       -   |    62        72        82        92       102       112   |     -|      132       142       152       162       172       182       192       202       212    
                                  20             35       44          56                                                         116    123
   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 2W53)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W53)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: TetR_C (33)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8KLP4_STEMA | Q8KLP4)
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: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
    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 2w53)
 

(-) 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
  2w53
    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
  Q8KLP4_STEMA | Q8KLP4
    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
  Q8KLP4_STEMA | Q8KLP4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8KLP4_STEMA | Q8KLP4: 3p9t

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W53)