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(-) Description

Title :  BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYLORI STRAIN 17875 IN COMPLEX WITH NANOBODY NB-ER14
 
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) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,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, C
    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-ER14
    Chains: B, 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): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:76 , THR A:77 , LYS A:78 , ASN A:79 , LYS C:200binding site for residue SO4 A 501
2AC2SOFTWAREASN A:109 , GLN A:113 , LYS C:175binding site for residue SO4 A 502
3AC3SOFTWARESER A:115 , THR A:116 , SER A:117 , GLU A:192 , GLY A:193binding site for residue SO4 A 503
4AC4SOFTWARESER C:115 , THR C:116 , SER C:117 , GLY C:193binding site for residue SO4 C 501
5AC5SOFTWARETHR A:217 , ILE A:218 , ASP A:219 , LYS C:251binding site for residue SO4 C 502
6AC6SOFTWARESER A:286 , TYR C:128 , ARG C:129 , LYS C:285 , GLN C:417 , PHE C:419binding site for residue SO4 C 503
7AC7SOFTWARELYS A:200 , ASP C:76 , THR C:77 , LYS C:78 , ASN C:79binding site for residue SO4 C 504
8AC8SOFTWARELYS C:237 , GLY C:238 , THR C:240binding site for residue SO4 C 505

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:106 -A:135
2A:189 -A:197
3A:277 -A:299
4A:395 -A:423
5B:22 -B:95
6B:105 -B:108
7C:106 -C:135
8C:189 -C:197
9C:277 -C:299
10C:395 -C:423
11D:22 -D:95
12D:105 -D:108

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:292 -Pro A:293
2Glu C:292 -Pro C:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F7L)

(-) Exons   (0, 0)

(no "Exon" information available for 5F7L)

(-) 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:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh.......eeeeeeee..eeeeeeeeeeee............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7l A  58 AINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTIDGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKSSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVN 459
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  ||   355       365       375       385       395   ||  414       424       434       444       454     
                                                                                                                                                                                                                                                                                                          330|                                               399|                                                  
                                                                                                                                                                                                                                                                                                           349                                                409                                                  


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..ee......eeeeeeeee....eeeeeeeee......eeeeeee...eeee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee.hhh........ee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7l B   1 QVQLQESGGGLVQPGGSLRLSCAASGSIYSLIAMGWYRQAPGKEHELVATISSGSTTYYADSVKGRFTISRDNAKNTLYLQMNSLKPEDTAMYYCAAYSDRLTDCSNCEADYWGQGTQVTV 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain C from PDB  Type:PROTEIN  Length:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh.......eeeeeeee..eeeeeeeeeeee............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7l C  58 AINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTIDGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNF 460
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  ||   355       365       375       385       395  ||   415       425       435       445       455     
                                                                                                                                                                                                                                                                                                          330|                                              398|                                                   
                                                                                                                                                                                                                                                                                                           349                                               409                                                   


Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eee.....eeeeeeeee....eeeeeeeee......eeeeeee...eeee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee.hhh........ee...eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7l D   1 QVQLQESGGGLVQPGGSLRLSCAASGSIYSLIAMGWYRQAPGKEHELVATISSGSTTYYADSVKGRFTISRDNAKNTLYLQMNSLKPEDTAMYYCAAYSDRLTDCSNCEADYWGQGTQVTVSHH 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 5F7L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F7L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F7L)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5F7L)

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        O52269_HELPX | O52269: 5f7k 5f7m 5f7n 5f7w 5f7y 5f8q 5f8r 5f93 5f97 5f9a 5f9d

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