6S5R

Cfucosylated second generation peptide dendrimer SBD6 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 2.08 Angstrom resolution, incomplete structure

• PDB DOI: https://doi.org/10.2210/pdb6S5R/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa, synthetic construct
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-07-02 Released: 2019-08-21 
• Deposition Author(s): Baeriswyl, S., Stocker, A., Reymond, J.-L.
• Funding Organization(s): Swiss National Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.237 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

X-Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB

Baeriswyl, S., Javor, S., Stocker, A., Darbre, T., Reymond, J.-L.

(2019) Helv Chim Acta 

• DOI: https://doi.org/10.1002/hlca.201900178

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 49.4 kDa 
• Atom Count: 3,623 
• Modelled Residue Count: 460 
• Deposited Residue Count: 466 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin	A, B, C, D	115	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SBD6	E [auth F], F [auth H]	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZDC (Subject of Investigation/LOI)	I [auth A], K [auth A], O [auth C], R [auth H]	3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid C8 H14 O6 YTZUDUWVQZSKNN-OASCRQMUSA-N
CA	G [auth A], H [auth A], J [auth A], L [auth B], M [auth C], N [auth C], P [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPP	E [auth F], F [auth H]	L-PEPTIDE LINKING	C3 H8 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.237 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.003	α = 90
b = 91.003	β = 90
c = 315.583	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Baeriswyl, S., Stocker, A., Reymond, J.-L.

---

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description