5F7W - JenaLib

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Title :   BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYLORI STRAIN 17875 IN COMPLEX WITH BLOOD GROUP B LEWIS B HEPTASACCHARIDE

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 :   2.81

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
	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
	Synonym	:	BLOOD GROUP ANTIGEN BINDING ADHESIN (BABA)

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 (5, 14)

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	GLA	2	Ligand/Ion	ALPHA D-GALACTOSE
5	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (5, 7)

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	GLA	1	Ligand/Ion	ALPHA D-GALACTOSE
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (5, 7)

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	GLA	1	Ligand/Ion	ALPHA D-GALACTOSE
5	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 , GLY A:193 , ASN A:194 , ASP A:195 , SER A:198 , GLN A:207 , VAL A:231 , ASP A:233 , SER A:234 , GLN A:235 , SER A:244 , THR A:246	binding site for Poly-Saccharide residues BGC A 501 through FUC A 507
2	AC2	SOFTWARE	CYS A:189 , SER A:190 , GLY A:191 , GLU A:192 , GLY A:193 , ASN A:194 , ASP A:195 , SER A:198 , GLN A:207 , VAL A:231 , ASP A:233 , SER A:234 , GLN A:235 , SER A:244 , THR A:246 , CYS B:189 , SER B:190 , GLY B:191 , GLU B:192 , GLY B:193 , ASN B:194 , ASP B:195 , SER B:198 , GLN B:207 , VAL B:231 , ASP B:233 , SER B:234 , GLN B:235 , ARG B:242 , SER B:244 , TYR B:245 , THR B:246	binding site for Poly-Saccharide residues BGC B 501 through FUC B 507

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	Glu B:292	-	Pro B:293
3	Leu C:99	-	Pro C:100
4	Leu D:99	-	Pro D:100

(no "SAP(SNP)/Variant" information available for 5F7W)

(no "PROSITE Motif" information available for 5F7W)

(no "Exon" information available for 5F7W)

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:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.ee...........eeeeeeeee..eeeeee............eehhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh.......eeee.........eeeeeeeee............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7w A  35 NLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTIDGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGS 462
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394   ||  413       423       433       443       453         
                                                                                                                                                                                                                                                                                                                                                                                                     398|                                                      
                                                                                                                                                                                                                                                                                                                                                                                                      408

Chain B from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeee.......hhhhhh.......eeee........eeeeeeeee............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7w B  35 NLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTIDKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSH 463
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    || 225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395  ||   414       424       434       444       454         
                                                                                                                                                                                                                  219|                                                                                                                                                                              398|                                                       
                                                                                                                                                                                                                   221                                                                                                                                                                               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...ee....eeeeeeeehhhhhh..eeeeeee.....eeeeeee.....eee.......eeeeee....eeeeeee..hhhhheeeeeeee.........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 5f7w 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...ee....eeeeeeeehhhhhh..eeeeeee.....eeeeeee.....eee.......eeeeee....eeeeeee..hhhhheeeeeeee.........eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5f7w 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 5F7W)

(no "CATH Domain" information available for 5F7W)

(no "Pfam Domain" information available for 5F7W)

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(no "Gene Ontology" information available for 5F7W)

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	Cis Peptide Bonds
		Glu A:292 - Pro A:293	[ RasMol ]
		Glu B:292 - Pro B:293	[ RasMol ]
		Leu C:99 - Pro C:100	[ RasMol ]
		Leu D:99 - Pro D:100	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (2, 2)

SS Bonds (10, 10)

Cis Peptide Bonds (4, 4)

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