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(-) Description

Title :  BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYLORI STRAIN P436 IN COMPLEX WITH BLOOD GROUP H LEWIS B HEXASACCHARIDE
 
Authors :  K. Moonens, P. Gideonsson, S. Subedi, E. Romao, S. Oscarson, S. Muylder T. Boren, H. Remaut
Date :  09 Dec 15  (Deposition) - 20 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Adhesin, Lectin, Nanobody, Complex, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Moonens, P. Gideonsson, S. Subedi, J. Bugaytsova, E. Romao, M. Mendez, J. Norden, M. Fallah, L. Rakhimova, A. Shevtsova, M. Lahmann, G. Castaldo, K. Brannstrom, F. Coppens, A. W. Lo, T. Ny, J. V. Solnick, G. Vandenbussche, S. Oscarson, L. Hammarstrom, A. Arnqvist, D. E. Berg, S. Muyldermans, T. Boren, H. Remaut
Structural Insights Into Polymorphic Abo Glycan Binding By Helicobacter Pylori.
Cell Host Microbe V. 19 55 2016
PubMed-ID: 26764597  |  Reference-DOI: 10.1016/J.CHOM.2015.12.004

(-) Compounds

Molecule 1 - ADHESIN BINDING FUCOSYLATED HISTO-BLOOD GROUP ANTIGEN, ADHESIN,ADHESIN BINDING FUCOSYLATED HISTO-BLOOD GROUP ANTIGEN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Variant: TOP10
    Gene: BABA2, BABA
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Other Details: IN THIS HYBRID CONSTRUCT THE INSERTION DOMAIN OF THE PERUVIAN STRAIN P436 (RESIDUES 179 TO 258, RESPONSIBLE FOR CARBOHYDRATE BINDING) WAS GRAFTED INTO THE FRAMEWORK OF THE GENERALIST STRAIN 17875
 
Molecule 2 - NANOBODY NB-ER19
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Variant: WK6
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3GLC1Ligand/IonALPHA-D-GLUCOSE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:189 , SER A:190 , GLY A:191 , GLY A:192 , ASN A:194 , ARG A:209 , GLN A:235 , ALA A:240 , ALA A:241 , THR A:243 , HOH A:1101 , HOH A:1120binding site for Poly-Saccharide residues GLC A 1001 through FUC A 1006

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:106 -A:135
2A:189 -A:197
3A:274 -A:296
4A:392 -A:420
5C:23 -C:96

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:207 -Gly A:208
2Glu A:289 -Pro A:290
3Leu C:99 -Pro C:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F9A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F9A)

(-) Exons   (0, 0)

(no "Exon" information available for 5F9A)

(-) 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:418
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh.........eeeeeeee..eeeeeeeeeeee.......eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f9a A  34 ENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTINVEYTYTCSGGGNTNCDPSLFGIGGDGRNGGSVTKTQTIDGKQVNTTISSKVVQPPHSAAYTEITNALNGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSH 460
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393 ||    412       422       432       442       452        
                                                                                                                                                                                                                                                                                                                                                                                                   395|                                                       
                                                                                                                                                                                                                                                                                                                                                                                                    405                                                       


Chain C from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee.....eeeeeeehhhhhh...eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee..........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 5f9a C   3 VQLQESGGGLVQPGGSLRLSCAASGSIFSGNVMGWYRQAPGKLREWVAAITPQGVPNYADSVKGRFTISRDNAKNMLYLQMSSLKPEDTALYYCNRLPNYRSWGQGTQVTVSS 115
                                    12        22        32        42        52        62        72        82        92       102       112
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  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 5F9A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F9A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F9A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5F9A)

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  Cis Peptide Bonds
    Asp A:207 - Gly A:208   [ RasMol ]  
    Glu A:289 - Pro A:290   [ RasMol ]  
    Leu C:99 - Pro C:100   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        O52269_HELPX | O52269: 5f7k 5f7l 5f7m 5f7n 5f7w 5f7y 5f8q 5f8r 5f93 5f97 5f9d
        Q6DT10_HELPX | Q6DT10: 5f9d

(-) Related Entries Specified in the PDB File

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