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 APO ZEBRAFISH ILEAL BILE ACID-BINDING PROTEIN
 
Authors :  S. Capaldi, G. Saccomani, D. Fessas, M. Signorelli, M. Perduca, H. L. Mo
Date :  23 Sep 08  (Deposition) - 13 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Ileal Bile Acid-Bindign Protein, Zebrafish, Cholic Acid, Lipid- Binding, Transport, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Capaldi, G. Saccomani, D. Fessas, M. Signorelli, M. Perduca, H. L. Monaco
The X-Ray Structure Of Zebrafish (Danio Rerio) Ileal Bile Acid-Binding Protein Reveals The Presence Of Binding Sites On The Surface Of The Protein Molecule.
J. Mol. Biol. V. 385 99 2009
PubMed-ID: 18952094  |  Reference-DOI: 10.1016/J.JMB.2008.10.007

(-) Compounds

Molecule 1 - ILEAL BILE ACID-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE50
    Expression System Strain: SG13009
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: FATTY ACID BINDING PROTEIN 6, ILEAL (GASTROTROPIN)

 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
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:49 , ASN A:61 , ILE A:92 , HOH A:208 , HOH A:255 , HOH A:299BINDING SITE FOR RESIDUE EDO A 200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:-1 -Ser A:0

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ELX)

(-) 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:134
 aligned with Q6IMW5_DANRE | Q6IMW5 from UniProtKB/TrEMBL  Length:131

    Alignment length:134
                             1                                                                                                                               131  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129 |  
         Q6IMW5_DANRE     - -MAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKV--   -
               SCOP domains d3elxa_ A: automated matches                                                                                                           SCOP domains
               CATH domains 3elxA00 A:-1-132  [code=2.40.128.20, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhh.....eeeeeee..eeeeeeeehhheeeeeeee....eeee.....eeee..eee..eeeee....eeeeeee..eeeeeeeee....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3elx A  -1 GSAFNGKWETESQEGYEPFCKLIGIPDDVIAKGRDFKLVTEIVQNGDDFTWTQYYPNNHVVTNKFIVGKESDMETVGGKKFKGIVSMEGGKLTISFPKYQQTTEISGGKLVETSTASGAQGTAVLVRTSKKVLV 132
                                     8        18        28        38        48        58        68        78        88        98       108       118       128
   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 3ELX)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6IMW5_DANRE | Q6IMW5)
molecular function
    GO:0032052    bile acid binding    Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0008206    bile acid metabolic process    The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
    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: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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:-1 - Ser A:0   [ RasMol ]  
 

(-) 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
  3elx
    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
  Q6IMW5_DANRE | Q6IMW5
    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
  Q6IMW5_DANRE | Q6IMW5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q6IMW5_DANRE | Q6IMW5: 3elz 3em0

(-) Related Entries Specified in the PDB File

3elz CRYSTAL STRUCTURE OF ZEBRAFISH ILEAL BILE ACID-BINDIN PROTEIN COMPLEXED WITH CHOLIC ACID (CRYSTAL FORM A).
3em0 CRYSTAL STRUCTURE OF ZEBRAFISH ILEAL BILE ACID-BINDIN PROTEIN COMPLEXED WITH CHOLIC ACID (CRYSTAL FORM B).