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(-) Description

Title :  PA-IIL LECTIN FROM PSEUDOMONAS AERUGINOSA COMPLEXED WITH FUCOSE-DERIVED GLYCOMIMETICS
 
Authors :  S. Beha, K. Marotte, C. Sabin, E. P. Mitchell, A. Imberty, R. Roy
Date :  22 May 08  (Deposition) - 21 Jul 09  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sugar-Binding Protein, Lectin, Fucose, Glycomimetics, Cystic Fibrosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Beha, K. Marotte, C. Sabin, E. P. Mitchell, A. Imberty, R. Roy
Fucose-Derived Glycomimetics As High Affinity Ligands For Bacterial Lectin Pa-Iil From Pseudomonas Aeruginosa
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FUCOSE-BINDING LECTIN PA-IIL
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI,
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET25PA2L
    Fragment: RESIDUES 2-115
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: PA-IIL LECTIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3SO42Ligand/IonSULFATE ION
4YX03Ligand/Ion[(3E)-3-(1-HYDROXYETHYLIDENE)-2,3-DIHYDROISOXAZOL-5-YL]METHYL 6-DEOXY-ALPHA-L-GALACTOPYRANOSIDE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:21 , SER A:22 , SER A:23 , GLU A:95 , ASP A:96 , ASP A:99 , ASP A:101 , ASP A:104 , CA A:990 , CA A:991 , HOH A:2046 , HOH A:2176 , GLY B:114BINDING SITE FOR RESIDUE FUC A 901
02AC2SOFTWAREASN A:21 , ASP A:101 , ASN A:103 , ASP A:104 , FUC A:901 , GLY B:114BINDING SITE FOR RESIDUE CA A 990
03AC3SOFTWAREGLU A:95 , ASP A:99 , ASP A:101 , ASP A:104 , FUC A:901BINDING SITE FOR RESIDUE CA A 991
04AC4SOFTWAREHOH A:2194 , HOH A:2195 , HOH A:2196 , ARG D:72BINDING SITE FOR RESIDUE SO4 A 998
05AC5SOFTWAREGLY A:114 , ASN B:21 , SER B:22 , SER B:23 , GLY B:24 , VAL B:69 , GLU B:95 , ASP B:96 , ASP B:99 , ASP B:101 , ASP B:104 , CA B:990 , CA B:991 , HOH B:2161 , HOH B:2173BINDING SITE FOR RESIDUE YX0 B 901
06AC6SOFTWARESER B:44 , ASN B:46 , ALA B:48 , HOH B:2174 , HOH B:2175 , HOH B:2176 , SER C:44 , THR C:45 , ASN C:46 , HOH C:2077BINDING SITE FOR RESIDUE SO4 B 970
07AC7SOFTWAREGLY A:114 , ASN B:21 , ASP B:101 , ASN B:103 , ASP B:104 , YX0 B:901BINDING SITE FOR RESIDUE CA B 990
08AC8SOFTWAREGLU B:95 , ASP B:99 , ASP B:101 , ASP B:104 , YX0 B:901BINDING SITE FOR RESIDUE CA B 991
09AC9SOFTWAREASN C:21 , SER C:22 , SER C:23 , GLY C:24 , VAL C:69 , GLU C:95 , ASP C:96 , ASP C:99 , ASP C:101 , ASP C:104 , CA C:990 , CA C:991 , HOH C:2146 , GLY D:114BINDING SITE FOR RESIDUE YX0 C 901
10BC1SOFTWAREGLU C:95 , ASP C:99 , ASP C:101 , ASP C:104 , YX0 C:901BINDING SITE FOR RESIDUE CA C 990
11BC2SOFTWAREASN C:21 , ASP C:101 , ASN C:103 , ASP C:104 , YX0 C:901 , GLY D:114BINDING SITE FOR RESIDUE CA C 991
12BC3SOFTWAREGLY C:114 , ASN D:21 , SER D:22 , SER D:23 , GLU D:95 , ASP D:96 , GLY D:97 , ASP D:99 , ASP D:101 , ASP D:104 , CA D:990 , CA D:991 , HOH D:2174 , HOH D:2193BINDING SITE FOR RESIDUE YX0 D 901
13BC4SOFTWAREGLY C:114 , ASN D:21 , ASP D:101 , ASN D:103 , ASP D:104 , YX0 D:901BINDING SITE FOR RESIDUE CA D 990
14BC5SOFTWAREGLU D:95 , ASP D:99 , ASP D:101 , ASP D:104 , YX0 D:901BINDING SITE FOR RESIDUE CA D 991

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Trp A:111 -Pro A:112
2Trp B:111 -Pro B:112
3Trp C:111 -Pro C:112
4Trp D:111 -Pro D:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VUC)

(-) 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:114
 aligned with Q9HYN5_PSEAE | Q9HYN5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HYN5_PSEAE     2 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 115
               SCOP domains d2vuca_ A: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.....eeeeeeeeeeeeeeeeeeee.............................eeeeeeee..ee......................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2vuc A   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110    


Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q9HYN5_PSEAE | Q9HYN5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HYN5_PSEAE     2 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 115
               SCOP domains d2vucb_ B: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.....eeeeeeeeeeeeeeeeeeee.............................eeeeeeee..ee......................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2vuc B   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110    


Chain C from PDB  Type:PROTEIN  Length:114
 aligned with Q9HYN5_PSEAE | Q9HYN5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HYN5_PSEAE     2 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 115
               SCOP domains d2vucc_ C: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..................eeeeeee..eeeeeeee...................eeeeeeee..ee......................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2vuc C   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110    


Chain D from PDB  Type:PROTEIN  Length:114
 aligned with Q9HYN5_PSEAE | Q9HYN5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HYN5_PSEAE     2 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 115
               SCOP domains d2vucd_ D: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----PA-IIL-2vucD01 D:6-113                                                                                      - Pfam domains (1)
           Pfam domains (2) -----PA-IIL-2vucD02 D:6-113                                                                                      - Pfam domains (2)
           Pfam domains (3) -----PA-IIL-2vucD03 D:6-113                                                                                      - Pfam domains (3)
           Pfam domains (4) -----PA-IIL-2vucD04 D:6-113                                                                                      - Pfam domains (4)
         Sec.struct. author .................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2vuc D   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PA-IIL] (21)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9HYN5_PSEAE | Q9HYN5)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9HYN5_PSEAE | Q9HYN5: 1gzt 1our 1ous 1oux 1ovp 1ovs 1oxc 1uzv 1w8f 1w8h 2boj 2bp6 2jdh 2jdk 2jdm 2jdn 2jdp 2jdu 2jdy 2vud 3dcq 3zdv 4ce8 5a3o 5d2a 5hch

(-) Related Entries Specified in the PDB File

1gzt PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) TOGETHER WITH FUCOSE
1our LECB (PA-LII) IN COMPLEX WITH MANNOSE
1ous LECB (PA-LII) CALCIUM-FREE
1oux LECB (PA-LII) SUGAR-FREE
1ovp LECB (PA-LII) IN COMPLEX WITH FRUCTOSE
1ovs LECB (PA-LII) IN COMPLEX WITH CORE TRIMANNOSIDE
1oxc LECB (PA-LII) IN COMPLEX WITH FUCOSE
1uzv HIGH AFFINITY FUCOSE BINDING OF PSEUDOMONAS AERUGINOSA LECTIN II: 1.0 E CRYSTAL STRUCTURE OF THE COMPLEX
1w43 STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LEWISA TRISACCHARIDE
1w8f PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) COMPLEXED WITH LACTO-N-NEO-FUCOPENTAOSE V( LNPFV)
1w8h STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LEWISA TRISACCHARIDE
2boj CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN (PA-IIL) COMPLEXED WITH METHYL-B-D -ARABINOPYRANOSIDE
2bp6 CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN (PA-IIL) COMPLEXED WITH A-L- GALACTOPYRANOSIDE
2jdh LECTIN PA-IIL OF P.AERUGINOSA COMPLEXED WITH DISACCHARIDE DERIVATIVE
2jdk LECTIN PA-IIL OF P.AERUGINOSA COMPLEXED WITH DISACCHARIDE DERIVATIVE
2jdm MUTANT (S22A) OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) COMPLEXED WITH METHYL-A-L- FUCOPYRANOSIDE
2jdn MUTANT (S22A) OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) COMPLEXED WITH METHYL-A-L- MANNOPYRANOSIDE
2jdp MUTANT (S23A) OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) COMPLEXED WITH METHYL-A-L- FUCOPYRANOSIDE
2jdu MUTANT (G24N) OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) COMPLEXED WITH METHYL-A-L- FUCOPYRANOSIDE
2jdy MUTANT (G24N) OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) COMPLEXED WITH METHYL-B-D- MANNOYRANOSIDE
2vud PA-IIL LECTIN FROM PSEUDOMONAS AERUGINOSA COMPLEXED WITH FUCOSE-DERIVED GLYCOMIMETICS