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 :  ENGINEERED LIPOCALIN DIGA16 IN COMPLEX WITH DIGOXIGENIN
 
Authors :  I. P. Korndoerfer, A. Skerra
Date :  25 Apr 02  (Deposition) - 17 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Pieris Brassicae, Lipocalin, Anticalin, Genetical Engineering, Digoxigenin, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. P. Korndoerfer, S. Schlehuber, A. Skerra
Structural Mechanism Of Specific Ligand Recognition By A Lipocalin Tailored For The Complexation Of Digoxigenin.
J. Mol. Biol. V. 330 385 2003
PubMed-ID: 12823976  |  Reference-DOI: 10.1016/S0022-2836(03)00573-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIGA16
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBBP21-DIGA16
    Expression System Strain: JM83
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: LARGE CABBAGE WHITE
    Organism Scientific: PIERIS BRASSICAE
    Organism Taxid: 7116
    Other Details: GENETICALLY ENGINEERED VARIANT OF BILIN BINDING PROTEIN
    Synonym: BILIN BINDING PROTEIN, BBP, DIGA16 ANTICALIN

 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
1DOG1Ligand/IonDIGOXIGENIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:28 , HIS A:35 , TYR A:39 , TYR A:47 , ARG A:58 , HIS A:86 , PHE A:114 , TRP A:129 , LEU A:131 , HOH A:502 , HOH A:523BINDING SITE FOR RESIDUE DOG A 500

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:115

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LKE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LKE)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.BBP_PIEBR31-44  1A:16-29

(-) Exons   (0, 0)

(no "Exon" information available for 1LKE)

(-) 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:157
 aligned with BBP_PIEBR | P09464 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:162
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179  
            BBP_PIEBR    20 DGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLIGSPVVDSQKLVYSDFS 181
               SCOP domains d1lkea_ A: Bilin-binding protein                                                                                                                                   SCOP domains
               CATH domains 1lkeA00 A:5-166  [code=2.40.128.20, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------Lipocalin-1lkeA01 A:23-166                                                                                                                       Pfam domains
         Sec.struct. author .............hhhhh.eeeeeeeehhhhhhhhheeeeeeeeee..eeeeeeeeee..eeeeeeeeeee..hhhh.eeeeeeee..eeeeeeeeeeee....eeeeeeee.-----..eeeeeeee.....hhhhhhhhhhhhhhh...hhhhhee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------LIPOCALIN     ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lke A   5 DGACPEVKPVDNFDWSQYHGKWWQVAAYPDHITKYGKCGWAEYTPEGKSVKVSRYSVIHGKEYFSEGTAYPVGDSKIGKIYHSYTIGGVTQEGVFNVLSTDNKNYIIGYFCSY-----GHMDLVWVLSRSMVLTGEAKTAVENYLIGSPVVDSQKLVYSDFS 166
                                    14        24        34        44        54        64        74        84        94       104       114  |    124       134       144       154       164  
                                                                                                                                          117   123
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BBP_PIEBR | P09464)
molecular function
    GO:0031409    pigment binding    Interacting selectively and non-covalently with a pigment, any general or particular coloring matter in living organisms, e.g. melanin.
biological process
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
    DOG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1lke)
 

(-) 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
  1lke
    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
  BBP_PIEBR | P09464
    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
  BBP_PIEBR | P09464
    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
        BBP_PIEBR | P09464: 1bbp 1kxo 1lnm 1n0s 1t0v

(-) Related Entries Specified in the PDB File

1bbp BILIN-BINDING PROTEIN
1kxo ENGINEERED LIPOCALIN DIGA16: APO-FORM
1n0s ENGINEERED LIPOCALIN FLUA IN COMPLEX WITH FLUORESCEIN