5AJC

X-ray structure of RSL lectin in complex with sialyl lewis X tetrasaccharide

• PDB DOI: https://doi.org/10.2210/pdb5AJC/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Ralstonia solanacearum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-20 Released: 2016-03-02 
• Deposition Author(s): Topin, J., Arnaud, J., Varrot, A., Imberty, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.187 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 31.86 kDa 
• Atom Count: 2,610 
• Modelled Residue Count: 267 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE FUCOSE-BINDING LECTIN PROTEIN	A, B, C	90	Ralstonia solanacearum	Mutation(s): 0
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum) Explore A0A0S4TLR1  Go to UniProtKB:  A0A0S4TLR1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose	D	3		N/A
Glycosylation Resources
GlyTouCan:  G51591NI GlyCosmos:  G51591NI GlyGen:  G51591NI

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N/A
Glycosylation Resources
GlyTouCan:  G80587NA GlyCosmos:  G80587NA GlyGen:  G80587NA

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose	F	4		N/A
Glycosylation Resources
GlyTouCan:  G07675NG GlyCosmos:  G07675NG GlyGen:  G07675NG

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	I [auth B], K [auth C]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
FUL	H [auth A], J [auth B], L [auth C]	beta-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-KGJVWPDLSA-N
TRS	G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900120	D	Lewis X antigen, alpha anomer	Oligosaccharide / Antigen

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900122	F	Sialyl-Lewis X antigen, alpha anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.187 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.766	α = 90
b = 83.163	β = 90
c = 90.697	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: 2016-03-02 
Deposition Author(s): Topin, J., Arnaud, J., Varrot, A., Imberty, A.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2016-07-27
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary