Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA LECTIN (BCLA) COMPLEXED WITH AMAN1-3MAN DISACCHARIDE
 
Authors :  E. Lameignere, T. C. Shiao, R. Roy, M. Wimmerova, F. Dubreuil, A. Varrot A. Imberty
Date :  01 Sep 09  (Deposition) - 15 Sep 09  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Sugar Binding Protein, Bacterial Lectin, Oligosaccharides (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Lameignere, T. C. Shiao, R. Roy, M. Wimmerova, F. Dubreuil, A. Varrot, A. Imberty
Structural Basis Of The Affinity For Oligomannosides And Analogs Displayed By Bc2L-A, A Burkholderia Cenocepacia Soluble Lectin.
Glycobiology V. 20 87 2010
PubMed-ID: 19770128  |  Reference-DOI: 10.1093/GLYCOB/CWP151

(-) Compounds

Molecule 1 - LECTIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 2-129
    Organism ScientificBURKHOLDERIA CENOCEPACIA
    Organism Taxid216591
    Other DetailsBURKHOLDERIA CENOCEPACIA STRAIN J2315 OBTAINED FROM THE CZECH COLLECTION OF MICROORGANISMS AT BRNO
    StrainJ2315
    SynonymBCLA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2MAN5Ligand/IonALPHA-D-MANNOSE
3SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MAN2Ligand/IonALPHA-D-MANNOSE
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MAN3Ligand/IonALPHA-D-MANNOSE
3SO43Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:28 , ASP A:115 , ASN A:117 , ASP A:118 , MAN A:1129 , GLY B:128BINDING SITE FOR RESIDUE CA A1131
02AC2SOFTWAREGLU A:109 , ASP A:113 , ASP A:115 , ASP A:118 , MAN A:1129BINDING SITE FOR RESIDUE CA A1132
03AC3SOFTWAREGLU B:109 , ASP B:113 , ASP B:115 , ASP B:118 , HOH B:2103BINDING SITE FOR RESIDUE CA B1129
04AC4SOFTWAREGLY A:128 , ASN B:28 , ASP B:115 , ASN B:117 , ASP B:118BINDING SITE FOR RESIDUE CA B1130
05AC5SOFTWAREASN C:28 , ALA C:29 , ALA C:30 , GLU C:31 , ASP C:110 , HIS C:112 , ASP C:113 , ASP C:115 , ASP C:118 , CA C:1130 , CA C:1131 , HOH C:2118 , HOH C:2119 , GLY D:128BINDING SITE FOR RESIDUE MAN C1129
06AC6SOFTWAREASN C:28 , ASP C:115 , ASN C:117 , ASP C:118 , MAN C:1129 , GLY D:128BINDING SITE FOR RESIDUE CA C1130
07AC7SOFTWAREGLU C:109 , ASP C:113 , ASP C:115 , ASP C:118 , MAN C:1129BINDING SITE FOR RESIDUE CA C1131
08AC8SOFTWAREGLU D:109 , ASP D:113 , ASP D:115 , ASP D:118 , MAN D:1129BINDING SITE FOR RESIDUE CA D1131
09AC9SOFTWAREGLY C:128 , ASN D:28 , ASP D:115 , ASN D:117 , ASP D:118 , MAN D:1129BINDING SITE FOR RESIDUE CA D1132
10BC1SOFTWAREALA B:29 , ALA B:30 , GLU B:31 , ASP B:110 , HIS B:112 , HOH B:2102 , HOH B:2103BINDING SITE FOR RESIDUE SO4 B1131
11BC2SOFTWAREHIS B:34 , LYS B:36 , TYR B:48 , SO4 B:1134 , HOH B:2104 , HOH B:2105 , HOH B:2106BINDING SITE FOR RESIDUE SO4 B1132
12BC3SOFTWAREHIS B:49 , LYS B:50 , ARG B:58 , HOH B:2108 , HOH B:2109BINDING SITE FOR RESIDUE SO4 B1133
13BC4SOFTWARELYS B:50 , SO4 B:1132 , HOH B:2017 , HOH B:2110BINDING SITE FOR RESIDUE SO4 B1134
14BC5SOFTWAREARG C:58 , HOH C:2120 , HOH C:2121BINDING SITE FOR RESIDUE SO4 C1132
15BC6SOFTWAREHIS D:49 , LYS D:50 , ARG D:58 , HOH D:2043BINDING SITE FOR RESIDUE SO4 D1133
16BC7SOFTWAREHIS C:49 , LYS C:50 , ARG C:58 , HOH C:2055BINDING SITE FOR RESIDUE SO4 C1133
17BC8SOFTWAREASN A:28 , ALA A:29 , ALA A:30 , GLU A:31 , GLU A:109 , ASP A:110 , HIS A:112 , ASP A:113 , ASP A:115 , ASP A:118 , CA A:1131 , CA A:1132 , HOH A:2111 , HOH A:2112 , HOH A:2113 , HOH A:2114 , GLY B:128BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1129 TO 1130
18BC9SOFTWAREGLY C:128 , HOH C:2117 , ASN D:28 , ALA D:29 , ALA D:30 , GLU D:31 , GLU D:109 , ASP D:110 , HIS D:112 , ASP D:113 , ASP D:115 , ASP D:118 , CA D:1131 , CA D:1132 , HOH D:2112 , HOH D:2113 , HOH D:2114 , HOH D:2115BINDING SITE FOR CHAIN D OF DI-SACCHARIDE MAN D1129 AND MAN D1130

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WR9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:125 -Pro A:126
2Trp B:125 -Pro B:126
3Trp C:125 -Pro C:126
4Trp D:125 -Pro D:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WR9)

(-) Exons   (0, 0)

(no "Exon" information available for 2WR9)

(-) Sequences/Alignments

Asymmetric 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:119
 aligned with B4EH87_BURCJ | B4EH87 from UniProtKB/TrEMBL  Length:129

    Alignment length:119
                                    20        30        40        50        60        70        80        90       100       110       120         
         B4EH87_BURCJ    11 AGEFSIPPNTDFRAIFFANAAEQQHIKLFIGDSQEPAAYHKLTTRDGPREATLNSGNGKIRFEVSVNGKPSATDARLAPINGKKSDGSPFTVNFGIVVSEDGHDSDYNDGIVVLQWPIG 129
               SCOP domains d2wr9a_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeee.....eeeeeee.......eeeeehhhhh.eeeeee....eeeeeeee.....eeeeee..eeeee....eeeeeeeeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2wr9 A  10 AGEFSIPPNTDFRAIFFANAAEQQHIKLFIGDSQEPAAYHKLTTRDGPREATLNSGNGKIRFEVSVNGKPSATDARLAPINGKKSDGSPFTVNFGIVVSEDGHDSDYNDGIVVLQWPIG 128
                                    19        29        39        49        59        69        79        89        99       109       119         

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with B4EH87_BURCJ | B4EH87 from UniProtKB/TrEMBL  Length:129

    Alignment length:123
                                    16        26        36        46        56        66        76        86        96       106       116       126   
         B4EH87_BURCJ     7 SSNRAGEFSIPPNTDFRAIFFANAAEQQHIKLFIGDSQEPAAYHKLTTRDGPREATLNSGNGKIRFEVSVNGKPSATDARLAPINGKKSDGSPFTVNFGIVVSEDGHDSDYNDGIVVLQWPIG 129
               SCOP domains d2wr9b_ B: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ee.....ee.....eeeeeeee.....eeeeeee......eeeeeehhhhh.eeeeee....eeeeeeee.....eeeeee..eeeee....eeeeeeeeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wr9 B   6 SSNRAGEFSIPPNTDFRAIFFANAAEQQHIKLFIGDSQEPAAYHKLTTRDGPREATLNSGNGKIRFEVSVNGKPSATDARLAPINGKKSDGSPFTVNFGIVVSEDGHDSDYNDGIVVLQWPIG 128
                                    15        25        35        45        55        65        75        85        95       105       115       125   

Chain C from PDB  Type:PROTEIN  Length:121
 aligned with B4EH87_BURCJ | B4EH87 from UniProtKB/TrEMBL  Length:129

    Alignment length:121
                                    18        28        38        48        58        68        78        88        98       108       118       128 
         B4EH87_BURCJ     9 NRAGEFSIPPNTDFRAIFFANAAEQQHIKLFIGDSQEPAAYHKLTTRDGPREATLNSGNGKIRFEVSVNGKPSATDARLAPINGKKSDGSPFTVNFGIVVSEDGHDSDYNDGIVVLQWPIG 129
               SCOP domains d2wr9c_ C: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeeee.....eeeeeee......eeeeeehhhhh.eeeeee....eeeeeeee.....eeeeee..eeeee....eeeeeeeeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wr9 C   8 NRAGEFSIPPNTDFRAIFFANAAEQQHIKLFIGDSQEPAAYHKLTTRDGPREATLNSGNGKIRFEVSVNGKPSATDARLAPINGKKSDGSPFTVNFGIVVSEDGHDSDYNDGIVVLQWPIG 128
                                    17        27        37        47        57        67        77        87        97       107       117       127 

Chain D from PDB  Type:PROTEIN  Length:124
 aligned with B4EH87_BURCJ | B4EH87 from UniProtKB/TrEMBL  Length:129

    Alignment length:124
                                    15        25        35        45        55        65        75        85        95       105       115       125    
         B4EH87_BURCJ     6 TSSNRAGEFSIPPNTDFRAIFFANAAEQQHIKLFIGDSQEPAAYHKLTTRDGPREATLNSGNGKIRFEVSVNGKPSATDARLAPINGKKSDGSPFTVNFGIVVSEDGHDSDYNDGIVVLQWPIG 129
               SCOP domains d2wr9d_ D: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------PA-IIL-2wr9D01 D:13-127                                                                                            - Pfam domains (1)
           Pfam domains (2) --------PA-IIL-2wr9D02 D:13-127                                                                                            - Pfam domains (2)
           Pfam domains (3) --------PA-IIL-2wr9D03 D:13-127                                                                                            - Pfam domains (3)
           Pfam domains (4) --------PA-IIL-2wr9D04 D:13-127                                                                                            - Pfam domains (4)
         Sec.struct. author .ee.....ee.....eeeeeeee.....eeeeeee......eeeeeehhhhh.eeeeee....eeeeeeee.....eeeeee..eeeee....eeeeeeeeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wr9 D   5 TSSNRAGEFSIPPNTDFRAIFFANAAEQQHIKLFIGDSQEPAAYHKLTTRDGPREATLNSGNGKIRFEVSVNGKPSATDARLAPINGKKSDGSPFTVNFGIVVSEDGHDSDYNDGIVVLQWPIG 128
                                    14        24        34        44        54        64        74        84        94       104       114       124    

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WR9)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (B4EH87_BURCJ | B4EH87)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 Visualization

(-) Interactive Views

Asymmetric 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:125 - Pro A:126   [ RasMol ]  
    Trp B:125 - Pro B:126   [ RasMol ]  
    Trp C:125 - Pro C:126   [ RasMol ]  
    Trp D:125 - Pro D:126   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2wr9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  B4EH87_BURCJ | B4EH87
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  B4EH87_BURCJ | B4EH87
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B4EH87_BURCJ | B4EH872vnv 2wra

(-) Related Entries Specified in the PDB File

2wra BCLA LECTIN FROM BURKHOLDERIA CENOCEPACIA COMPLEXED WITH AMAN1(AMAN1-6)-3MAN TRISACCHARIDE