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(-) Description

Title :  BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYLORI STRAIN 17875 IN COMPLEX WITH NANOBODY NB-ER19
 
Authors :  K. Moonens, P. Gideonsson, S. Subedi, E. Romao, S. Oscarson, S. Muylder T. Boren, H. Remaut
Date :  08 Dec 15  (Deposition) - 20 Jan 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
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
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Variant: TOP10
    Gene: BABA2
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Variant: 17875
 
Molecule 2 - NANOBODY NB-ER19
    Chains: C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NA1Ligand/IonSODIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION
3PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:189 , SER A:190 , GLY A:191 , ASN A:194 , THR A:246binding site for residue PO4 A 501
2AC2SOFTWAREASN A:124 , GLN A:164 , GLY A:412 , HOH A:674binding site for residue EDO A 502
3AC3SOFTWAREGLU C:47 , TRP C:48 , HOH C:315binding site for residue NA C 201

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:106 -A:135
2A:189 -A:197
3A:277 -A:299
4A:395 -A:423
5B:106 -B:135
6B:189 -B:197
7B:277 -B:299
8B:395 -B:423
9C:23 -C:96
10D:23 -D:96

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:292 -Pro A:293
2Leu C:99 -Pro C:100
3Glu B:292 -Pro B:293
4Leu D:99 -Pro D:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F7K)

(-) Exons   (0, 0)

(no "Exon" information available for 5F7K)

(-) Sequences/Alignments

Asymmetric 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh.......eeeeee....eeeeeeeeee............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f7k A  32 NYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGS 462
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     ||223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393    || 412       422       432       442       452       462
                                                                                                                                                                                                                   217|                                                                                                                                                                               398|                                                      
                                                                                                                                                                                                                    220                                                                                                                                                                                408                                                      


Chain B from PDB  Type:PROTEIN  Length:421
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh.......eeeeee....eeeeeeeeee............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7k B  32 NYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSH 463
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     ||223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393    || 412       422       432       442       452       462 
                                                                                                                                                                                                                   217|                                                                                                                                                                               398|                                                       
                                                                                                                                                                                                                    220                                                                                                                                                                                408                                                       


Chain C from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeeeehhhhhh..eeeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 5f7k C   3 VQLQESGGGLVQPGGSLRLSCAASGSIFSGNVMGWYRQAPGKLREWVAAITPQGVPNYADSVKGRFTISRDNAKNMLYLQMSSLKPEDTALYYCNRLPNYRSWGQGTQVTVSS 115
                                    12        22        32        42        52        62        72        82        92       102       112   


Chain D from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeeeehhhhhh..eeeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5f7k D   3 VQLQESGGGLVQPGGSLRLSCAASGSIFSGNVMGWYRQAPGKLREWVAAITPQGVPNYADSVKGRFTISRDNAKNMLYLQMSSLKPEDTALYYCNRLPNYRSWGQGTQVTVSSH 116
                                    12        22        32        42        52        62        72        82        92       102       112
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  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 5F7K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F7K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F7K)

(-) Gene Ontology  (0, 0)

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        O52269_HELPX | O52269: 5f7l 5f7m 5f7n 5f7w 5f7y 5f8q 5f8r 5f93 5f97 5f9a 5f9d

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