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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH METHYL 6-(2,4,6-TRIMETHYLPHENYLSULFONYLAMIDO)-6-DEOXY-ALPHA-D-MANNOPYRANOSIDE
 
Authors :  D. Hauck, I. Joachim, B. Frommeyer, A. Varrot, B. Philipp, H. M. Moller, A. Imberty, T. E. Exner, A. Titz
Date :  30 Nov 12  (Deposition) - 18 Sep 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sugar Binding Protein, Glycomimetic, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Hauck, I. Joachim, B. Frommeyer, A. Varrot, B. Philipp, H. M. Moller A. Imberty, T. E. Exner, A. Titz
Discovery Of Two Classes Of Potent Glycomimetic Inhibitors Of Pseudomonas Aeruginosa Lecb With Distinct Binding Modes.
Acs Chem. Biol. V. 8 1775 2013
PubMed-ID: 23719508  |  Reference-DOI: 10.1021/CB400371R

(-) Compounds

Molecule 1 - FUCOSE-BINDING LECTIN PA-IIL
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET25PA2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET25B
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric/Biological Unit (6, 19)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3F1A4Ligand/Ion2,4,6-TRIMETHYLBENZENESULFONAMIDE
4GOL1Ligand/IonGLYCEROL
5MMA4Ligand/IonO1-METHYL-MANNOSE
6SO41Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:95 , ASP A:99 , ASP A:101 , ASP A:104 , MMA A:201BINDING SITE FOR RESIDUE CA A 199
02AC2SOFTWAREASN A:21 , ASP A:101 , ASN A:103 , ASP A:104 , MMA A:201 , GLY B:114BINDING SITE FOR RESIDUE CA A 200
03AC3SOFTWAREGLU B:95 , ASP B:99 , ASP B:101 , ASP B:104 , MMA B:201BINDING SITE FOR RESIDUE CA B 199
04AC4SOFTWAREGLY A:114 , ASN B:21 , ASP B:101 , ASN B:103 , ASP B:104 , MMA B:201BINDING SITE FOR RESIDUE CA B 200
05AC5SOFTWAREGLU C:95 , ASP C:99 , ASP C:101 , ASP C:104 , MMA C:201BINDING SITE FOR RESIDUE CA C 199
06AC6SOFTWAREASN C:21 , ASP C:101 , ASN C:103 , ASP C:104 , MMA C:201 , GLY D:114BINDING SITE FOR RESIDUE CA C 200
07AC7SOFTWAREGLU D:95 , ASP D:99 , ASP D:101 , ASP D:104 , MMA D:201BINDING SITE FOR RESIDUE CA D 199
08AC8SOFTWAREGLY C:114 , ASN D:21 , ASP D:101 , ASN D:103 , ASP D:104 , MMA D:201BINDING SITE FOR RESIDUE CA D 200
09AC9SOFTWAREGLN B:53 , VAL B:54 , HOH B:2057 , HOH B:2069 , HOH B:2116 , ALA D:38 , THR D:39 , GLN D:53BINDING SITE FOR RESIDUE GOL B 203
10BC1SOFTWARESER B:44 , ASN B:46 , ALA B:48 , HOH B:2065 , SER D:44 , THR D:45 , ASN D:46 , HOH D:2050 , HOH D:2053 , HOH D:2092BINDING SITE FOR RESIDUE SO4 D 204
11BC2SOFTWAREALA B:1 , HOH B:2117 , HOH B:2118 , ALA D:1BINDING SITE FOR RESIDUE EDO B1115
12BC3SOFTWAREARG A:13 , ASN A:21 , SER A:22 , SER A:23 , GLU A:95 , ASP A:96 , ASP A:99 , ASP A:101 , ASP A:104 , GLY A:114 , CA A:199 , CA A:200 , HOH A:2127 , HOH A:2134 , SER B:23 , THR B:45 , GLY B:114 , MMA B:201BINDING SITE FOR RESIDUES MMA A 201 AND F1A A 202
13BC4SOFTWAREGLY A:114 , F1A A:202 , ASN B:21 , SER B:22 , SER B:23 , GLY B:24 , GLU B:95 , ASP B:96 , ASP B:99 , ASP B:101 , ASP B:104 , CA B:199 , CA B:200 , HOH B:2105BINDING SITE FOR RESIDUES MMA B 201 AND F1A B 202
14BC5SOFTWAREASN C:21 , SER C:22 , SER C:23 , GLU C:95 , ASP C:96 , ASP C:99 , ASP C:101 , ASP C:104 , CA C:199 , CA C:200 , HOH C:2100 , HOH C:2109 , ASN D:70 , GLY D:114 , F1A D:202 , HOH D:2084BINDING SITE FOR RESIDUES MMA C 201 AND F1A C 202
15BC6SOFTWAREARG C:72 , GLY C:114 , F1A C:202 , ASN D:21 , SER D:22 , SER D:23 , GLU D:95 , ASP D:96 , ASP D:99 , ASP D:101 , ASP D:104 , CA D:199 , CA D:200 , HOH D:2086 , HOH D:2091BINDING SITE FOR RESIDUES MMA D 201 AND F1A D 202

(-) SS Bonds  (0, 0)

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

(-) 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 3ZDV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZDV)

(-) 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 d3zdva_ A: Fucose-binding lectin II (PA-LII)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee......eeeeeeee....eeeeeee..eeeeeeee...eeeeeeeeee......eeeeeeee.....eeeeeeeee...eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3zdv 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 d3zdvb_ B: Fucose-binding lectin II (PA-LII)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee......eeeeeeee....eeeeeee..eeeeeeee...eeeeeeeeee......eeeeeeee.....eeeeeeeee...eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3zdv 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 d3zdvc_ C: Fucose-binding lectin II (PA-LII)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee......eeeeeeee....eeeeeee..eeeeeeee...eeeeeeeeee......eeeeeeee.....eeeeeeeee...eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3zdv 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 d3zdvd_ D: Fucose-binding lectin II (PA-LII)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee......eeeeeeee....eeeeeee..eeeeeeee...eeeeeeeeee......eeeeeeee.....eeeeeeeee...eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3zdv 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 3ZDV)

(-) Pfam Domains  (0, 0)

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

(-) 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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  3zdv
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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 2vuc 2vud 3dcq 4ce8 5a3o 5d2a 5hch

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ZDV)