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 :  SALMONELLA ENTERICA SADA 483-523 FUSED TO GCN4 ADAPTORS ( SADAK3B-V2, OUT-OF-REGISTER FUSION)
 
Authors :  M. D. Hartmann, O. Ridderbusch, A. N. Lupas, B. Hernandez Alvarez
Date :  09 Aug 09  (Deposition) - 03 Nov 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Membrane Protein, Ion Coordination, Hydrophobic Core, Trimeric Autotransporter Adhesin, Taa, Stutter, Stammer, Coiled Coil, Protein Export, Polar Core Residues (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Hartmann, O. Ridderbusch, K. Zeth, R. Albrecht, O. Testa, D. N. Woolfson, G. Sauer, S. Dunin-Horkawicz, A. N. Lupas, B. H. Alvarez
A Coiled-Coil Motif That Sequesters Ions To The Hydrophobic Core.
Proc. Natl. Acad. Sci. Usa V. 106 16950 2009
PubMed-ID: 19805097  |  Reference-DOI: 10.1073/PNAS.0907256106

(-) Compounds

Molecule 1 - TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 483-523 FUSED TO GCN4 ADAPTORS
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Other Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:488 , ASN B:488 , ASN C:488BINDING SITE FOR RESIDUE CL A1554
2AC2SOFTWAREASN A:495 , ASN B:495 , ASN C:495BINDING SITE FOR RESIDUE CL A1555
3AC3SOFTWAREASN A:502 , ASN B:502 , ASN C:502BINDING SITE FOR RESIDUE CL C1554
4AC4SOFTWAREASN A:509 , ASN B:509 , ASN C:509BINDING SITE FOR RESIDUE CL A1556

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WPS)

(-) 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:98
 aligned with SADA_SALTY | Q8ZL64 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:217
                                   402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       
           SADA_SALTY   393 SINQNTTDIAANTTSINQNTTDIATNTTNINSLSDSVTTLTDDALLWDAASGAFSAKHNGSDSKITNLAAGTLAADSTDAVNGSQLFDTNEKVDQNTADITTNTNSINQNTTDIATNTTNINNLSDSITTLTDDALLWDAASGAFSANHNGSASKITNLAAGTLAADSTDAVNGSQLFATNENVSQNTADITTNTNSINQNTTDIATNTTSINNLSD 609
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wpsA00 A:456-553                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh---hhhh----hhhh--------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------------------------------------------hhhhhhhhhhhhhhhhhh---hhhh----hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wps A 456 QIEDKIEEILSKIYHIEN---EIAR----IKKL--------------------------------------------------------IEKVDQNTADITTNTNSINQNTTDIATNTTNINNLSDSITTLMK-------------------------------------------------QIEDKIEEILSKIYHIEN---EIAR----IKKLIK 553
                                   465       | - |  |  478  |      -         -         -         -         -       482       492       502       512       522  |      -         -         -         -         -  |    533       543   |  |  - |     
                                           473 474  |  478  |                                                      482                                        525                                               526              543 544  |  548     
                                                  477     481                                                                                                                                                                           547          


Chain B from PDB  Type:PROTEIN  Length:98
 aligned with SADA_SALTY | Q8ZL64 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:217
                                   402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       
           SADA_SALTY   393 SINQNTTDIAANTTSINQNTTDIATNTTNINSLSDSVTTLTDDALLWDAASGAFSAKHNGSDSKITNLAAGTLAADSTDAVNGSQLFDTNEKVDQNTADITTNTNSINQNTTDIATNTTNINNLSDSITTLTDDALLWDAASGAFSANHNGSASKITNLAAGTLAADSTDAVNGSQLFATNENVSQNTADITTNTNSINQNTTDIATNTTSINNLSD 609
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wpsB00 B:456-553                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh---hhhh----hhhh--------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------------------------------------------hhhhhhhhhhhhhhhhhh---hhhh----hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wps B 456 QIEDKIEEILSKIYHIEN---EIAR----IKKL--------------------------------------------------------IEKVDQNTADITTNTNSINQNTTDIATNTTNINNLSDSITTLMK-------------------------------------------------QIEDKIEEILSKIYHIEN---EIAR----IKKLIK 553
                                   465       | - |  |  478  |      -         -         -         -         -       482       492       502       512       522  |      -         -         -         -         -  |    533       543   |  |  - |     
                                           473 474  |  478  |                                                      482                                        525                                               526              543 544  |  548     
                                                  477     481                                                                                                                                                                           547          


Chain C from PDB  Type:PROTEIN  Length:98
 aligned with SADA_SALTY | Q8ZL64 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:217
                                   402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       
           SADA_SALTY   393 SINQNTTDIAANTTSINQNTTDIATNTTNINSLSDSVTTLTDDALLWDAASGAFSAKHNGSDSKITNLAAGTLAADSTDAVNGSQLFDTNEKVDQNTADITTNTNSINQNTTDIATNTTNINNLSDSITTLTDDALLWDAASGAFSANHNGSASKITNLAAGTLAADSTDAVNGSQLFATNENVSQNTADITTNTNSINQNTTDIATNTTSINNLSD 609
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wpsC00 C:456-553                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh---hhhh----hhhh--------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------------------------------------------hhhhhhhhhhhhhhhhhh---hhhh----hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wps C 456 QIEDKIEEILSKIYHIEN---EIAR----IKKL--------------------------------------------------------IEKVDQNTADITTNTNSINQNTTDIATNTTNINNLSDSITTLMK-------------------------------------------------QIEDKIEEILSKIYHIEN---EIAR----IKKLIK 553
                                   465       | - |  |  478  |      -         -         -         -         -       482       492       502       512       522  |      -         -         -         -         -  |    533       543   |  |  - |     
                                           473 474  |  478  |                                                      482                                        525                                               526              543 544  |  548     
                                                  477     481                                                                                                                                                                           547
   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 2WPS)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (SADA_SALTY | Q8ZL64)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wps)
 

(-) 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
  2wps
    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
  SADA_SALTY | Q8ZL64
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  SADA_SALTY | Q8ZL64
    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
        SADA_SALTY | Q8ZL64: 2wpq 2wpr 2yny 2ynz 2yo0 2yo1 2yo2 2yo3 3zmf

(-) Related Entries Specified in the PDB File

2wpq SALMONELLA ENTERICA SADA 479-519 FUSED TO GCN4 ADAPTORS (SADAK3, IN-REGISTER FUSION)
2wpr SALMONELLA ENTERICA SADA 483-523 FUSED TO GCN4 ADAPTORS (SADAK3B-V1, OUT-OF-REGISTER FUSION)
2wpy GCN4 LEUCINE ZIPPER MUTANT WITH ONE VXXNXXX MOTIF COORDINATING CHLORIDE
2wpz GCN4 LEUCINE ZIPPER MUTANT WITH TWO VXXNXXX MOTIFS COORDINATING CHLORIDE
2wq0 GCN4 LEUCINE ZIPPER MUTANT WITH THREE IXXNTXX MOTIFS COORDINATING CHLORIDE
2wq1 GCN4 LEUCINE ZIPPER MUTANT WITH THREE IXXNTXX MOTIFS COORDINATING BROMIDE
2wq2 GCN4 LEUCINE ZIPPER MUTANT WITH THREE IXXNTXX MOTIFS COORDINATING IODIDE
2wq3 GCN4 LEUCINE ZIPPER MUTANT WITH THREE IXXNTXX MOTIFS COORDINATING CHLORIDE AND NITRATE