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(-) Description

Title :  LECTIN PA-IIL OF P.AERUGINOSA COMPLEXED WITH DISACCHARIDE DERIVATIVE
 
Authors :  K. Marotte, C. Sabin, C. Preville, M. Pymbock, I. Deguise, M. Wimmerova, E. P. Mitchell, A. Imberty, R. Roy
Date :  09 Jan 07  (Deposition) - 24 Jul 07  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lectin, Cystic Fibrosis, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Marotte, C. Sabin, C. Preville, M. Pymbock, M. Wimmerova, E. P. Mitchell, A. Imberty, R. Roy
X-Ray Structures And Thermodynamics Of The Interaction Of Pa-Iil From Pseudomonas Aeruginosa With Disaccharide Derivatives.
Chemmedchem V. 2 1328 2007
PubMed-ID: 17623286  |  Reference-DOI: 10.1002/CMDC.200700100
(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
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: PA-IIL

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2FUC4Ligand/IonALPHA-L-FUCOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO41Ligand/IonSULFATE ION
5TA53Ligand/Ion2H-1,2,3-TRIAZOL-4-YLMETHANOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN B:43 , SER B:44 , ASN B:46 , ALA B:48 , HOH B:2099 , SER C:44 , THR C:45 , ASN C:46 , HOH C:2084 , HOH C:2169 , HOH C:2170BINDING SITE FOR RESIDUE SO4 C1115
02AC2SOFTWAREASN 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:1116 , CA A:1117 , HOH A:2172 , GLY B:114BINDING SITE FOR RESIDUE FUC A1115
03AC3SOFTWAREGLU B:95 , ASP B:99 , ASP B:101 , ASP B:104 , FUC B:1115BINDING SITE FOR RESIDUE CA B1118
04AC4SOFTWAREASN A:21 , ASP A:101 , ASN A:103 , ASP A:104 , FUC A:1115 , GLY B:114BINDING SITE FOR RESIDUE CA A1116
05AC5SOFTWAREGLU A:95 , ASP A:99 , ASP A:101 , ASP A:104 , FUC A:1115BINDING SITE FOR RESIDUE CA A1117
06AC6SOFTWAREGLY C:114 , ASN D:21 , ASP D:101 , ASN D:103 , ASP D:104 , FUC D:1115BINDING SITE FOR RESIDUE CA D1118
07AC7SOFTWAREGLU D:95 , ASP D:99 , ASP D:101 , ASP D:104 , FUC D:1115BINDING SITE FOR RESIDUE CA D1119
08AC8SOFTWAREASN C:21 , ASP C:101 , ASN C:103 , ASP C:104 , FUC C:1118 , GLY D:114BINDING SITE FOR RESIDUE CA C1116
09AC9SOFTWAREGLU C:95 , ASP C:99 , ASP C:101 , ASP C:104 , FUC C:1118BINDING SITE FOR RESIDUE CA C1117
10BC1SOFTWAREGLY A:114 , ASN B:21 , ASP B:101 , ASN B:103 , ASP B:104 , FUC B:1115BINDING SITE FOR RESIDUE CA B1119
11BC2SOFTWAREGLY A:114 , ASN B:21 , SER B:22 , SER B:23 , GLU B:95 , ASP B:96 , GLY B:97 , ASP B:99 , ASP B:101 , ASP B:104 , CA B:1118 , CA B:1119 , HOH B:2169 , HOH B:2182 , HOH B:2183 , HOH B:2184 , HOH B:2185BINDING SITE FOR POLY-SACCHARIDE RESIDUES FUC B1115 THROUGH TA5 B1117
12BC3SOFTWAREGLY A:114 , ASN B:21 , SER B:23 , GLU B:95 , ASP B:96 , GLY B:97 , ASP B:99 , ASP B:101 , ASN B:103 , ASP B:104 , FUC B:1115 , HOH B:2182 , HOH B:2183 , HOH B:2184 , HOH B:2185 , ASN C:21 , SER C:22 , SER C:23 , GLU C:95 , ASP C:96 , GLY C:97 , ASP C:99 , ASP C:101 , ASN C:103 , ASP C:104 , HOH C:2158 , HOH C:2171 , HOH C:2172 , HOH C:2173 , HOH C:2175 , HOH C:2176 , HOH C:2177 , GLY D:114BINDING SITE FOR POLY-SACCHARIDE RESIDUES FUC C1118 THROUGH TA5 C1120
13BC4SOFTWAREGLN B:43 , SER B:44 , ASN B:46 , ALA B:48 , HOH B:2099 , ASN C:21 , SER C:23 , SER C:44 , THR C:45 , ASN C:46 , GLU C:95 , ASP C:96 , GLY C:97 , ASP C:99 , ASP C:101 , ASN C:103 , ASP C:104 , GLY C:114 , FUC C:1118 , HOH C:2084 , HOH C:2169 , HOH C:2170 , HOH C:2171 , HOH C:2172 , HOH C:2173 , HOH C:2175 , HOH C:2176 , HOH C:2177 , 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 , GLY D:114 , CA D:1118 , HOH D:2170 , HOH D:2184 , HOH D:2185BINDING SITE FOR POLY-SACCHARIDE RESIDUES FUC D1115 THROUGH TA5 D1117

(-) SS Bonds  (0, 0)

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

(-) 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 2JDH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2JDH)

(-) 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 d2jdha_ A: automated matches                                                                                       SCOP domains
               CATH domains 2jdhA00 A:1-114 Calcium-mediated lectin                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.....eeeeeeeeeeeeeeeeeeee.............................eeeeeeee..ee......................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2jdh 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 d2jdhb_ B: automated matches                                                                                       SCOP domains
               CATH domains 2jdhB00 B:1-114 Calcium-mediated lectin                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.....eeeeeeeeeeeeeeeeeeee.............................eeeeeeee..ee......................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2jdh 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 d2jdhc_ C: automated matches                                                                                       SCOP domains
               CATH domains 2jdhC00 C:1-114 Calcium-mediated lectin                                                                            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
                 2jdh 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 d2jdhd_ D: automated matches                                                                                       SCOP domains
               CATH domains 2jdhD00 D:1-114 Calcium-mediated lectin                                                                            CATH domains
           Pfam domains (1) -----PA-IIL-2jdhD01 D:6-113                                                                                      - Pfam domains (1)
           Pfam domains (2) -----PA-IIL-2jdhD02 D:6-113                                                                                      - Pfam domains (2)
           Pfam domains (3) -----PA-IIL-2jdhD03 D:6-113                                                                                      - Pfam domains (3)
           Pfam domains (4) -----PA-IIL-2jdhD04 D:6-113                                                                                      - Pfam domains (4)
         Sec.struct. author .................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2jdh 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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) 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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  2jdh
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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 2jdk 2jdm 2jdn 2jdp 2jdu 2jdy 2vuc 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