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 :  F17A-G LECTIN DOMAIN WITH BOUND GLCNAC(BETA1-O)PARANITROPHENYL LIGAND
 
Authors :  L. Buts, A. De Boer, J. D. M. Olsson, W. Jonckheere, M. De Kerpel, E. De Y. Guerardel, R. Willaert, L. Wyns, M. Wuhrer, S. Oscarson, H. De Grev J. Bouckaert
Date :  05 Nov 08  (Deposition) - 10 Nov 09  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Bacterial Adhesin, Lectin, Bacterial Attachment, Pathogenesis, Immunoglobulin Fold, Cell Projection, Fimbrium, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Lonardi, K. Moonens, L. Buts, A. R. De Boer, J. D. M. Olsson, M. S. Weiss, E. Fabre, Y. Guerardel, A. M. Deelder, S. Oscarson, M. Wuhrer, J. Bouckaert
Structural Sampling Of Glycan Interaction Profiles Reveals Mucosal Receptors For Fimbrial Adhesins Of Enterotoxigenic Escherichia Coli
Biology V. 2 894 2013
PubMed: search  |  Reference-DOI: 10.3390/BIOLOGY2030894

(-) Compounds

Molecule 1 - F17A-G
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHD52
    Expression System Strain: BL21-AI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CARBOHYDRATE-BINDING DOMAIN, UNP RESIDUES 23-199
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1LEC1Ligand/IonN-[(2S,3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-2-(4-NITROPHENOXY)OXAN-3-YL]ETHANAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:43 , ASN A:44 , VAL A:65 , GLY A:75 , LEU A:76 , THR A:77 , GLU A:78 , ASP A:88 , THR A:89 , TRP A:109 , THR A:118 , GLN A:119 , GLY A:120 , HOH A:201 , HOH A:303 , HOH A:330BINDING SITE FOR RESIDUE LEC A 178

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:53 -A:110

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F64)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F64)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F64)

(-) Exons   (0, 0)

(no "Exon" information available for 3F64)

(-) 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:168
 aligned with F17AG_ECOLX | Q99003 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:175
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     
          F17AG_ECOLX    23 AVSFIGSTENDVGPSLGSYSRTHAMDNLPFVYDTRNKIGYQNANVWHISKGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGDTKYSRGTAMSGNSWENVFSGWCVGANTASTQGLSVRVTPVILKRNSSARYSVQKTSIGSIRMRPYNGSSAGSVQTTVNFSLNPFTLN 197
               SCOP domains d3f64a_ A: Fimbrial a       dhesin F17-AG lectin domain                                                                                                                         SCOP domains
               CATH domains 3f64A00 A:1-175 Bacte       rial adhesins - F17c-type                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeee....eee..-------.ee.......eeeeeeeeeee...eeeeeeee...eeeee..eeeee....eeeeeeee..hhhhhee......eeeeeeee.....eeeeeeeeeeeeee........eee..eeeeeeeeeee..........eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f64 A   1 AVSFIGSTENDVGPSLGSYSR-------PFVYDTRNKIGYQNANVWHISKGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGDTKYSRGTAMSGNSWENVFSGWCVGANTASTQGLSVRVTPVILKRNSSARYSVQKTSIGSIRMRPYNGSSAGSVQTTVNFSLNPFTLN 175
                                    10        20|       30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
                                               21      29
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F64)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (F17AG_ECOLX | Q99003)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0044406    adhesion of symbiont to host    The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    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:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

 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
    LEC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3f64)
 

(-) 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
  3f64
    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
  F17AG_ECOLX | Q99003
    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
  F17AG_ECOLX | Q99003
    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
        F17AG_ECOLX | Q99003: 1o9v 1o9w 1o9z 1zpl 2bsc 3f6j

(-) Related Entries Specified in the PDB File

1o9z F17G APOPROTEIN