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(-) Description

Title :  BIFUNCTIONAL DENDRIMERS
 
Authors :  G. Michaud, R. Visini, A. Stocker, T. Darbre, J. L. Reymond
Date :  05 Aug 15  (Deposition) - 10 Feb 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Lectinb, Pseudomonas, Dendrimer, Biofilm, Bifunctional, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Michaud, R. Visini, M. Bergmann, G. Salerno, R. Bosco, E. Gillon, B. Richichi, C. Nativi, A. Imberty, A. Stocker, T. Darbre, J. -L. Reymond
Overcoming Antibiotic Resistance In Pseudomonas Aeruginosa Biofilms Using Glycopeptide Dendrimers
Chem Sci V. 7 166 2016
PubMed: search  |  Reference-DOI: 10.1039/C5SC03635F

(-) Compounds

Molecule 1 - FUCOSE-BINDING LECTIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LECB, ERS445055_01627, PA8380_17510, PAE221_03716, PAMH19_1713, YQ19_10010
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: FUCOSE-BINDING LECTIN PA-IIL,PHOTOPEXIN A,PSEUDOMONAS AERUGINOSA GENOME ASSEMBLY PAE221
 
Molecule 2 - ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL
    Chains: D, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GAL1Ligand/IonBETA-D-GALACTOSE
3PHB1Ligand/IonP-HYDROXYBENZOIC ACID
4ZDC2Ligand/Ion3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:95 , ASP A:99 , ASP A:101 , ASP A:104 , ZDC E:101binding site for residue CA A 201
2AC2SOFTWAREASN A:21 , ASP A:101 , ASN A:103 , ASP A:104 , GLY B:114 , ZDC E:101binding site for residue CA A 202
3AC3SOFTWAREGLU B:95 , ASP B:99 , ASP B:101 , ASP B:104 , CA B:202 , ZDC D:101binding site for residue CA B 201
4AC4SOFTWAREGLY A:114 , ASN B:21 , ASP B:101 , ASN B:103 , ASP B:104 , CA B:201 , ZDC D:101binding site for residue CA B 202
5AC5SOFTWAREGLY A:71 , ARG A:72 , PRO A:73 , PRO C:2 , ALA C:3 , PHE C:6 , CYS C:7binding site for Poly-Saccharide residues ALA C 1 through GAL C 102
6AC6SOFTWAREGLY A:114 , ASN B:21 , SER B:22 , SER B:23 , GLU B:95 , ASP B:96 , ASP B:99 , ASP B:101 , ASP B:104 , CA B:201 , CA B:202 , PRO D:3binding site for Di-peptide ZDC D 101 and ALA D 2
7AC7SOFTWAREASN 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:201 , CA A:202 , GLY B:114 , PRO E:3binding site for Di-peptide ZDC E 101 and ALA E 2

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1C:7 -C:7

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D2A)

(-) Exons   (0, 0)

(no "Exon" information available for 5D2A)

(-) 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
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee.....eeeeeeee.....eeeeeeeee...eeeeeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5d2a A   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110    


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee.....eeeeeeee..ee.eeeeeeeee...eeeeeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5d2a B   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110    


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               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
                 5d2a C   1 APAKFC   7
                              ||  
                              3|  
                               5  


Chain D from PDB  Type:PROTEIN  Length:3
                                   
               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
                 5d2a D   2 APA   4


Chain E from PDB  Type:PROTEIN  Length:3
                                   
               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
                 5d2a E   2 APA   4
   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  (0, 0)

(no "SCOP Domain" information available for 5D2A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D2A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D2A)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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        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 3zdv 4ce8 5a3o 5hch

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