5A6Y

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with mannose-alpha1,3mannoside

• PDB DOI: https://doi.org/10.2210/pdb5A6Y/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa UCBPP-PA14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-02 Released: 2016-05-25 
• Deposition Author(s): Sommer, R., Wagner, S., Varrot, A., Khaledi, A., Haussler, S., Imberty, A., Titz, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.163 
• R-Value Work: 0.122 
• R-Value Observed: 0.125 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.42 kDa 
• Atom Count: 4,141 
• Modelled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOSE-BINDING LECTIN PA-IIL	A, B, C, D	114	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0
UniProt
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore A0A0H2ZE85  Go to UniProtKB:  A0A0H2ZE85

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	E, F, G	2		N/A
Glycosylation Resources
GlyTouCan:  G00891MP GlyCosmos:  G00891MP GlyGen:  G00891MP

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	J [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4	P [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	H [auth A], I [auth A], L [auth B], M [auth B], N [auth C], O [auth C], Q [auth D], R [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900112	E, F, G	3alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.163 
• R-Value Work: 0.122 
• R-Value Observed: 0.125 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.979	α = 90
b = 49.779	β = 93.34
c = 75.438	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Sommer, R., Wagner, S., Varrot, A., Khaledi, A., Haussler, S., Imberty, A., Titz, A.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2020-01-22
  Changes: Derived calculations, Other, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: 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