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 PA-IL LECTIN COMPLEXED WITH GALBG0 AT 1.5 A RESOLUTION
 
Authors :  R. U. Kadam, M. Bergmann, M. Hurley, D. Garg, M. Cacciarini, M. A. Swider C. Nativi, M. Sattler, A. R. Smyth, P. Williams, M. Camara, A. Stocker, J. -L. Reymond
Date :  23 Aug 11  (Deposition) - 21 Sep 11  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,I,J
Keywords :  Sugar Binding Protein-Inhibitor Complex, Adhesin, Glycosphingolipid-Antigen, Galactose-Specific, Galactosides (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. U. Kadam, M. Bergmann, M. Hurley, D. Garg, M. Cacciarini, M. A. Swiderska, C. Nativi, M. Sattler, A. R. Smyth, P. Williams, M. Camara, A. Stocker, T. Darbre, J. -L. Reymond
A Glycopeptide Dendrimer Inhibitor Of The Galactose Specific Lectin Leca And Of Pseudomonas Aeruginosa Biofilms
Angew. Chem. Int. Ed. Engl. V. 50 10631 2011
PubMed-ID: 21919164  |  Reference-DOI: 10.1002/ANIE.201104342

(-) Compounds

Molecule 1 - PA-I GALACTOPHILIC LECTIN
    Atcc: 208964
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET25PAIL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET25
    Expression System Vector Type: PLASMID
    Fragment: MAINLY BETA SANDWICH
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: PA-IL, GALACTOSE-BINDING LECTIN, LECTIN LECA
 
Molecule 2 - CARBOXYPROPYL-BETA-THIOGALACTOSIDE-LYS-PRO-LEUNH2
    Chains: I, J
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2G0S2Mod. Amino Acid3-(BETA-D-GALACTOPYRANOSYLTHIO)PROPANOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:36 , ASP A:100 , THR A:104 , ASN A:107 , ASN A:108 , G0S I:1BINDING SITE FOR RESIDUE CA A1123
2AC2SOFTWARETYR B:36 , ASP B:100 , THR B:104 , ASN B:107 , ASN B:108 , G0S J:1BINDING SITE FOR RESIDUE CA B1123
3AC3SOFTWARETYR A:36 , HIS A:50 , GLN A:53 , ASP A:100 , THR A:104 , ASN A:107 , CA A:1123 , HOH A:2260 , HOH A:2342 , HOH A:2343 , HOH A:2344BINDING SITE FOR CHAIN I OF CARBOXYPROPYL-BETA-THIOGALACTOSIDE-LYS-PRO-LEUNH2
4AC4SOFTWARETYR B:36 , HIS B:50 , GLN B:53 , ASP B:100 , THR B:104 , ASN B:107 , CA B:1123 , HOH B:2164 , HOH B:2203 , HOH B:2210 , HOH B:2300 , HOH B:2301BINDING SITE FOR CHAIN J OF CARBOXYPROPYL-BETA-THIOGALACTOSIDE-LYS-PRO-LEUNH2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZYH)

(-) 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:121
 aligned with PA1L_PSEAE | Q05097 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           PA1L_PSEAE     2 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 122
               SCOP domains d3zyha_ A: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.....eeeeeeeeee.............................eeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zyh A   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA1L_PSEAE | Q05097 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           PA1L_PSEAE     2 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 122
               SCOP domains d3zyhb_ B: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.....eeeeeeeeee.............................eeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zyh B   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain I from PDB  Type:PROTEIN  Length:1
                          2      
               SCOP domains - SCOP domains
               CATH domains - CATH domains
               Pfam domains - Pfam domains
         Sec.struct. author . Sec.struct. author
                 SAPs(SNPs) - SAPs(SNPs)
                    PROSITE - PROSITE
                 Transcript - Transcript
                 3zyh I   1 x   1
                                                                                                                                                     |
                                                                                                                                                     1-G0S


Chain J from PDB  Type:PROTEIN  Length:1
                          2      
               SCOP domains - SCOP domains
               CATH domains - CATH domains
               Pfam domains - Pfam domains
         Sec.struct. author . Sec.struct. author
                 SAPs(SNPs) - SAPs(SNPs)
                    PROSITE - PROSITE
                 Transcript - Transcript
                 3zyh J   1 x   1
                             |
                             |
                             1-G0S
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZYH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA1L_PSEAE | Q05097)
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:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    G0S  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3zyh)
 

(-) 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
  3zyh
    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
  PA1L_PSEAE | Q05097
    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
  PA1L_PSEAE | Q05097
    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
        PA1L_PSEAE | Q05097: 1l7l 1oko 1uoj 2vxj 2wyf 3zyb 3zyf 4a6s 4al9 4cp9 4cpb 4ljh 4lk6 4lk7 4lkd 4lke 4lkf 4yw6 4yw7 4ywa 5d21

(-) Related Entries Specified in the PDB File

1l7l CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN 1DETERMINED BY SINGLE WAVELENGTH ANOMALOUS SCATTERINGPHASING METHOD
1oko CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN 1 COMPLEXED WITH GALACTOSE AT 1.6 A RESOLUTION
1uoj CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN 1 IN THE CALCIUM-FREE STATE
2vxj CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL13BGAL14GLC AT 1.9 A RESOLUTION
2wyf CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL12BGAL-O-MET AT 2.4 A RESOLUTION
3zyb CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALAG0 AT 2.3 A RESOLUTION
3zyf CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH NPG AT 1.9 A RESOLUTION