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 :  CRYSTAL STRUCTURE OF B.SUBTILIS ANTI-TRAP PROTEIN, AN ANTAGONIST OF TRAP-RNA INTERACTIONS
 
Authors :  M. B. Shevtsov, Y. Chen, P. Gollnick, A. A. Antson
Date :  26 Jul 05  (Deposition) - 30 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Keywords :  Transcription Regulation, Anti-Trap (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. B. Shevtsov, Y. Chen, P. Gollnick, A. A. Antson
Crystal Structure Of Bacillus Subtilis Anti-Trap Protein, An Antagonist Of Trap/Rna Interaction.
Proc. Natl. Acad. Sci. Usa V. 102 17600 2005
PubMed-ID: 16306262  |  Reference-DOI: 10.1073/PNAS.0508728102

(-) Compounds

Molecule 1 - TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
    ChainsA, B, C, D, E, F, G, H, I, J, K, L
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17AT
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA
    Expression System VectorPET17B
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymANTI-TRAP, AT

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric/Biological Unit ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1ZN12Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:12 , CYS A:15 , CYS A:26 , CYS A:29BINDING SITE FOR RESIDUE ZN A1054
02AC2SOFTWARECYS B:12 , CYS B:15 , CYS B:26 , CYS B:29BINDING SITE FOR RESIDUE ZN B1054
03AC3SOFTWARECYS C:12 , CYS C:15 , CYS C:26 , CYS C:29BINDING SITE FOR RESIDUE ZN C1054
04AC4SOFTWARECYS D:12 , CYS D:15 , CYS D:26 , CYS D:29BINDING SITE FOR RESIDUE ZN D1054
05AC5SOFTWARECYS E:12 , CYS E:15 , CYS E:26 , CYS E:29BINDING SITE FOR RESIDUE ZN E1054
06AC6SOFTWARECYS F:12 , CYS F:15 , CYS F:26 , CYS F:29BINDING SITE FOR RESIDUE ZN F1054
07AC7SOFTWARECYS G:12 , CYS G:15 , CYS G:26 , CYS G:29BINDING SITE FOR RESIDUE ZN G1054
08AC8SOFTWARECYS H:12 , CYS H:15 , CYS H:26 , CYS H:29BINDING SITE FOR RESIDUE ZN H1054
09AC9SOFTWARECYS I:12 , CYS I:15 , CYS I:26 , CYS I:29BINDING SITE FOR RESIDUE ZN I1054
10BC1SOFTWARECYS J:12 , CYS J:15 , CYS J:26 , CYS J:29BINDING SITE FOR RESIDUE ZN J1054
11BC2SOFTWARECYS K:12 , CYS K:15 , CYS K:26 , CYS K:29BINDING SITE FOR RESIDUE ZN K1054
12BC3SOFTWARECYS L:12 , CYS L:15 , CYS L:26 , CYS L:29BINDING SITE FOR RESIDUE ZN L1054

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BX9)

(-) Exons   (0, 0)

(no "Exon" information available for 2BX9)

(-) 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:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 A  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain B from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 B  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain C from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 C  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain D from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 D  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain E from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 E  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain F from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 F  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain G from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 G  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain H from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 H  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain I from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 I  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain J from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 J  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain K from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 K  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

Chain L from PDB  Type:PROTEIN  Length:53
 aligned with RTPA_BACSU | O31466 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RTPA_BACSU    1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhheee........ee..ee........eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bx9 L  1 MVIATDDLEVACPKCERAGEIEGTPCPACSGKGVILTAQGYTLLDFIQKHLNK 53
                                    10        20        30        40        50   

   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 2BX9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BX9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BX9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K,L   (RTPA_BACSU | O31466)
molecular function
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2bx9)
 

(-) 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
  2bx9
    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
  RTPA_BACSU | O31466
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  RTPA_BACSU | O31466
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RTPA_BACSU | O314662ko8 2zp8 2zp9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2BX9)