2VUD | pdb_00002vud

PA-IIL lectin from pseudomonas aeruginosa complexed with fucose- derived glycomimetics

• PDB DOI: https://doi.org/10.2210/pdb2VUD/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Milvago chimango chimango
• Mutation(s): No 


• Deposited: 2008-05-22 Released: 2009-07-21 
• Deposition Author(s): Beha, S., Marotte, K., Sabin, C., Mitchell, E.P., Imberty, A., Roy, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Fucose-Derived Glycomimetics as High Affinity Ligands for Bacterial Lectin Pa-Iil from Pseudomonas Aeruginosa

Beha, S., Marotte, K., Sabin, C., Mitchell, E.P., Imberty, A., Roy, R.

To be published.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 48.48 kDa 
• Atom Count: 4,087 
• Modeled 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	Mutation(s): 0
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5  Go to UniProtKB:  Q9HYN5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LZ0	I [auth B], M [auth C], P [auth D]	[1-(2-oxoethyl)-1H-1,2,3-triazol-5-yl]methyl 6-deoxy-alpha-L-galactopyranoside C11 H17 N3 O6 VXMWUAUJLLGYLQ-GDWDKGMLSA-N
FUC	H [auth A]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
SO4	G [auth A], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	E [auth A], F [auth A], J [auth B], K [auth B], N [auth C], O [auth C], Q [auth D], R [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.079	α = 90
b = 73.179	β = 93.86
c = 55.367	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Beha, S., Marotte, K., Sabin, C., Mitchell, E.P., Imberty, A., Roy, R.

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-08
  Changes: Advisory, Source and taxonomy
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.5: 2023-12-13
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary