5F8R - JenaLib

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Title :   BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYLORI STRAIN S831 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. 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

Molecule 1 - ADHESIN BINDING FUCOSYLATED HISTO-BLOOD GROUP ANTIGEN, ADHESIN,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, BABA
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210
	Other Details	:	IN THIS HYBRID CONSTRUCT THE DIVERSITY LOOP 1 (DL1) OF THE SPANISH SPECIALIST STRAIN S831 WAS GRAFTED INTO THE FRAMEWORK OF THE GENERALIST STRAIN 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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	FUC	4	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	4	Ligand/Ion	BETA-D-GALACTOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:189 , SER A:190 , GLY A:191 , GLU A:192 , ASN A:194 , GLN A:207 , ASP A:233 , SER A:234 , SER A:244 , TYR A:245 , THR A:246	binding site for Poly-Saccharide residues BGC A 501 through FUC A 506
2	AC2	SOFTWARE	CYS A:189 , SER A:190 , GLY A:191 , GLU A:192 , ASN A:194 , GLN A:207 , ASP A:233 , SER A:234 , SER A:244 , TYR A:245 , THR A:246 , CYS B:189 , SER B:190 , GLY B:191 , GLU B:192 , ASN B:194 , GLN B:207 , ASP B:233 , SER B:234 , GLN B:235 , SER B:244 , TYR B:245 , THR B:246	binding site for Poly-Saccharide residues BGC B 501 through FUC B 506

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Glu A:292	-	Pro A:293
2	Gly B:210	-	Thr B:211
3	Ser B:286	-	Gly B:287
4	Glu B:292	-	Pro B:293
5	Leu C:99	-	Pro C:100
6	Leu D:99	-	Pro D:100

(no "SAP(SNP)/Variant" information available for 5F8R)

(no "PROSITE Motif" information available for 5F8R)

(no "Exon" information available for 5F8R)

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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.ee...........eeeeeeeee..eeeeee............eehhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh.......eeeeee....eeeeeeeeee............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f8r A  35 NLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCLPKVTGVDNQNGGTKTKTQTGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGS 462
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214  ||   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 ||    415       425       435       445       455       
                                                                                                                                                                                                                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 ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.ee...........eeeeeeeee..eeeeee............eehhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh........eeeeeee..eeeeeeeeeeee............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f8r B  33 YENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCLPKVTGVDNQNGGTKTKTQTIDGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGS 462
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392     ||411       421       431       441       451       461 
                                                                                                                                                                                                                                                                                                                                                                                                       398|                                                      
                                                                                                                                                                                                                                                                                                                                                                                                        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...eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee..........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 5f8r 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
                 5f8r D   3 VQLQESGGGLVQPGGSLRLSCAASGSIFSGNVMGWYRQAPGKLREWVAAITPQGVPNYADSVKGRFTISRDNAKNMLYLQMSSLKPEDTALYYCNRLPNYRSWGQGTQVTVSSH 116
                                    12        22        32        42        52        62        72        82        92       102       112

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 '\|'

(no "SCOP Domain" information available for 5F8R)

(no "CATH Domain" information available for 5F8R)

(no "Pfam Domain" information available for 5F8R)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 5F8R)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Glu A:292 - Pro A:293	[ RasMol ]
		Glu B:292 - Pro B:293	[ RasMol ]
		Gly B:210 - Thr B:211	[ RasMol ]
		Leu C:99 - Pro C:100	[ RasMol ]
		Leu D:99 - Pro D:100	[ RasMol ]
		Ser B:286 - Gly B:287	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (2, 2)

SS Bonds (10, 10)

Cis Peptide Bonds (6, 6)

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SAPs(SNPs)/Variants (0, 0)

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