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(-) Description

Title :  CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH NPG AT 1.9 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 :  22 Aug 11  (Deposition) - 21 Sep 11  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Adhesin, Glycosphingolipid-Antigen, Galactose-Specific, Galactosides, Sugar Binding Protein (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
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET25PAIL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET25
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: LECTIN LECA, PA-IL, GALACTOSE-BINDING LECTIN

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
11474Ligand/Ion1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
2CA4Ligand/IonCALCIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11472Ligand/Ion1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
11472Ligand/Ion1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:36 , ASP A:100 , THR A:104 , ASN A:107 , ASN A:108 , 147 A:1001BINDING SITE FOR RESIDUE CA A 901
2AC2SOFTWARETYR A:36 , HIS A:50 , GLN A:53 , ASP A:100 , THR A:104 , ASN A:107 , CA A:901 , HOH A:2055 , HOH A:2075 , HOH A:2119 , HIS D:50 , PRO D:51 , GLN D:53 , 147 D:1004BINDING SITE FOR RESIDUE 147 A1001
3AC3SOFTWARETYR B:36 , ASP B:100 , THR B:104 , ASN B:107 , ASN B:108 , 147 B:1002BINDING SITE FOR RESIDUE CA B 902
4AC4SOFTWARETYR B:36 , HIS B:50 , GLN B:53 , ASP B:100 , THR B:104 , ASN B:107 , CA B:902 , HOH B:2056 , HOH B:2089 , HOH B:2090 , GLY C:37 , PRO C:38 , ASN C:107 , 147 C:1003BINDING SITE FOR RESIDUE 147 B1002
5AC5SOFTWARETYR C:36 , ASP C:100 , THR C:104 , ASN C:107 , ASN C:108 , 147 C:1003BINDING SITE FOR RESIDUE CA C 903
6AC6SOFTWAREGLY B:37 , PRO B:38 , ASN B:107 , 147 B:1002 , TYR C:36 , HIS C:50 , GLN C:53 , ASP C:100 , THR C:104 , ASN C:107 , CA C:903 , HOH C:2062 , HOH C:2095 , HOH C:2096BINDING SITE FOR RESIDUE 147 C1003
7AC7SOFTWARETYR D:36 , ASP D:100 , THR D:104 , ASN D:107 , ASN D:108 , 147 D:1004BINDING SITE FOR RESIDUE CA D 904
8AC8SOFTWAREHIS A:50 , PRO A:51 , 147 A:1001 , TYR D:36 , HIS D:50 , GLN D:53 , ASP D:100 , THR D:104 , ASN D:107 , CA D:904 , HOH D:2056 , HOH D:2084 , HOH D:2085 , HOH D:2086BINDING SITE FOR RESIDUE 147 D1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZYF)

(-) 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: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 d3zyfa_ 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
                 3zyf 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 d3zyfb_ B: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.....eeeeeeeeee.........eee..............eeeeeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zyf B   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain C 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 d3zyfc_ C: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.....eeeeeeeeee.........eee..............eeeeeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zyf C   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain D 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 d3zyfd_ D: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.....eeeeeeeeee.........eee..............eeeeeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zyf D   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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).

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  3zyf
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  PA1L_PSEAE | Q05097
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 Related Entries

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

UniProtKB/Swiss-Prot
        PA1L_PSEAE | Q05097: 1l7l 1oko 1uoj 2vxj 2wyf 3zyb 3zyh 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 1 DETERMINED BY SINGLE WAVELENGTH ANOMALOUS SCATTERING PHASING 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
3zyh CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALBG0 AT 1.5 A RESOLUTION