5F97

Blood group antigen binding adhesin BabA of Helicobacter pylori strain A730 in complex with blood group A type 1 hexasaccharide

• PDB DOI: https://doi.org/10.2210/pdb5F97/pdb

• Classification: CELL ADHESION
• Organism(s): Helicobacter pylori, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-09 Released: 2016-01-20 
• Deposition Author(s): Moonens, K., Gideonsson, P., Subedi, S., Romao, E., Oscarson, S., Muyldermans, S., Boren, T., Remaut, H.
• Funding Organization(s): Flanders Institute of Biotechnology (VIB), Flanders Science Foundation (FWO), Hercules Foundation, Vetenskapsradet/VR, Cancerfonden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.237 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 257.1 kDa 
• Atom Count: 16,664 
• Modelled Residue Count: 2,160 
• Deposited Residue Count: 2,356 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen	A, B, C, D	469	Helicobacter pylori	Mutation(s): 0  Gene Names: babA2, babA
UniProt
Find proteins for Q6DSX7 (Helicobacter pylori) Explore Q6DSX7  Go to UniProtKB:  Q6DSX7
Find proteins for O52269 (Helicobacter pylori) Explore O52269  Go to UniProtKB:  O52269
UniProt Groups	O52269Q6DSX7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanbody Nb-ER19	E, F, G, H	120	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	I, J, K, L	6		N/A
Glycosylation Resources
GlyTouCan:  G82858KU GlyCosmos:  G82858KU GlyGen:  G82858KU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.237 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.9	α = 90
b = 134.91	β = 102.52
c = 123.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Moonens, K., Gideonsson, P., Subedi, S., Romao, E., Oscarson, S., Muyldermans, S., Boren, T., Remaut, H.

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Funding Organization	Location	Grant Number
Flanders Institute of Biotechnology (VIB)	Belgium	PRJ9
Flanders Science Foundation (FWO)	Belgium	Odysseus program
Hercules Foundation	Belgium	UABR/09/005
Vetenskapsradet/VR	Sweden	--
Cancerfonden	Sweden	--

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2016-09-28
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary