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 
- Funding Organization(s): Flanders Institute of Biotechnology (VIB), Flanders Science Foundation (FWO), Hercules Foundation, Vetenskapsradet/VR, Cancerfonden
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 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
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 | 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 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Groups | O52269Q6DSX7 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Nanbody Nb-ER19 | 120 | Lama glama | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
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.
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 (Full details and data files)
- 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