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 THE ALCALIGIN OUTER MEMBRANE RECEPTEUR FAUA FROM BORDETELLA PERTUSSIS
 
Authors :  K. Brillet, E. Lauber, C. Reimmann, S. K. Armstrong, D. Cobessi
Date :  09 Sep 08  (Deposition) - 31 Mar 09  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym./Biol. Unit :  A
Keywords :  Membrane Protein, Membrane Receptor, Membrane Transporter, Siderophore, Membrane, Receptor, Tonb Box (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Brillet, A. Meksem, E. Lauber, C. Reimmann, D. Cobessi
Use Of An In-House Approach To Study The Three-Dimensional Structures Of Various Outer Membrane Proteins: Structure Of The Alcaligin Outer Membrane Transporter Faua From Bordetella Pertussis
Acta Crystallogr. , Sect. D V. 65 326 2009
PubMed-ID: 19307713  |  Reference-DOI: 10.1107/S0907444909002200

(-) Compounds

Molecule 1 - FERRIC ALCALIGIN SIDEROPHORE RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 36-734
    Gene: FAUA, BP2463
    Organism Scientific: BORDETELLA PERTUSSIS
    Organism Taxid: 520
    Synonym: FAUA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

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
1AC1SOFTWARELYS A:461 , LYS A:463 , ASN A:491BINDING SITE FOR RESIDUE SO4 A 653
2AC2SOFTWAREARG A:383 , HOH A:745 , HOH A:778BINDING SITE FOR RESIDUE SO4 A 654

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EFM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EFM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EFM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EFM)

(-) Exons   (0, 0)

(no "Exon" information available for 3EFM)

(-) 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:572
 aligned with Q9X6A5_BORPT | Q9X6A5 from UniProtKB/TrEMBL  Length:734

    Alignment length:679
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725         
         Q9X6A5_BORPT    56 EISDLTEGTNAYTTEAMSTATGLTLSPRETPQSVSVVTRQQIEDQGLTDTGAILATAPGISVTRSDSNRYSFSARGFTIDNFQFDGLVSPILSQWNYGSTDMDAAIYDHVEIVRGATGLMTGSGNPSAAVNFVRKRPLREFAATFNASVGSWDYVRGDADISVPITEDGRIRSRLVAAYSQGDSYVHFLDTRRRTFYGVVSADLTPDTVLTTSVEYQHNHSNGFGSGFPLFYSDGSRTDFNRSVANNAPWARQDTEATTYFVDLTHRFTNDWKLRAAYSHTDGRYLMKHVYRGGYPDRHTGIIAAPPAFSNYDGNLDRDDIHFSLSAPFEAFGLRHEVALGWMSIDNHSDIQRYAMVGPAPAIGSFFDWRRAHIQEPSWADTLSPADDVRTKQTGAYLVGRFALAEPLHLIVGDRWSDWKTKQMYFGSRREYRIKNQFTPYAGLTYDINDTYTAYASYTEIFQPQNARDTSGGILPPIKSKSYELGLKAAYLEGRLNTSAALFQTRQDNLAQVIPGSSIPGFPNMQASRAASGAKVEGIDLEASGQILPDWNIGASYTHFTTKDASGNPINTNHPRSLFKLYTTYRLPGALHRLTVGGGVDWQSRMYQAAASPRGNVEVEQDSYALVSLMARFDFNKKLSATLNVNNLFDKKYYDQIGFYSQGWWGAPRNVMLNLRAQY 734
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------3efmA01 A:54-156 Ferric Hydroxamate Uptake Protein; Chain A, domain 1                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhh...eeeehhhhhhhh...hhhhhhhh....eee.......eeee..ee..eeee..eeee.hhhhh.hhhhhhhh.eeeeeeee..hhhhhh.....eeeeeee.......eeeeeeeee...eeeeeeeeeee......eeeeeeeeeeee.-----..eeeeeeeeeeeeeee..eeeeeeeeeeeeee..-------------------------....eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee.------------------.eeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee.-------------------------....eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeee....eeeeeeeeeeee..............eeeeeeeeeeeeeehhh.eeeeeeeeeeeee.eeee..............eeee...eeeeeeeeeeeeee..eeeeeeeeeeeee.............eeeeeeeeee.......eeeeeeeeeee..--------------...eeeeeeeeeeeee..eeeeeeee..--------------------.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3efm A  21 EISDLTEGTNAYTTEAMSTATGLTLSPRETPQSVSVVTRQQIEDQGLTDTGAILATAPGISVTRSDSNRYSFSARGFTIDNFQFDGLVSPILSQWNYGSTDMDAAIYDHVEIVRGATGLMTGSGNPSAAVNFVRKRPLREFAATFNASVGSWDYVRGDADISVPITEDGRIRSRLVAAYSQGD-----LDTRRRTFYGVVSADLTPDTVLTTSVEYQHNHSNG-------------------------PWARQDTEATTYFVDLTHRFTNDWKLRAAYSHTDGRYLMKHV------------------FSNYDGNLDRDDIHFSLSAPFEAFGLRHEVALGWMSIDNHSDIQRYAM-------------------------TLSPADDVRTKQTGAYLVGRFALAEPLHLIVGDRWSDWKTKQMYFGSRREYRIKNQFTPYAGLTYDINDTYTAYASYTEIFQPQNARDTSGGILPPIKSKSYELGLKAAYLEGRLNTSAALFQTRQDNLAQVIPGSSIPGFPNMQASRAASGAKVEGIDLEASGQILPDWNIGASYTHFTTKDASGNPINTNHPRSLFKLYTTYRLPGALHRLTVGGGVDWQSRM--------------QDSYALVSLMARFDFNKKLSATLNVNNL--------------------RNVMLNLRAQY 652
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  |    210       220       230       240  |      -         -       258       268       278       288       298         -       302       312       322       332       342     |   -         -         - |     372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     |   -         -|      603       613       | -         -       643         
                                                                                                                                                                                                                203   209                               243                       257                                      298                301                                            348                       364                                                                                                                                                                                                                             588            594                        621                  642
   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 3EFM)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EFM)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9X6A5_BORPT | Q9X6A5)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0015891    siderophore transport    The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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 3efm)
 

(-) 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
  3efm
    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
  Q9X6A5_BORPT | Q9X6A5
    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
  Q9X6A5_BORPT | Q9X6A5
    Protein Disorder Prediction: DisEMBL | 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 3EFM)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3EFM)