5CGB | pdb_00005cgb

Crystal structure of FimH in complex with heptyl alpha-D-septanoside

• PDB DOI: https://doi.org/10.2210/pdb5CGB/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-09 Released: 2016-07-20 
• Deposition Author(s): Jakob, R.P., Preston, R.P., Zihlmann, P., Fiege, B., Sager, C.P., Vannam, R., Rabbani, S., Zalewski, A., Maier, T., Ernst, B., Peczuh, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

The price of flexibility - a case study on septanoses as pyranose mimetics.

Sager, C.P., Fiege, B., Zihlmann, P., Vannam, R., Rabbani, S., Jakob, R.P., Preston, R.C., Zalewski, A., Maier, T., Peczuh, M.W., Ernst, B.

(2018) Chem Sci 9: 646-654

• PubMed: 29629131 
• DOI: https://doi.org/10.1039/c7sc04289b
• Primary Citation Related Structures: 
  5CGB


• PubMed Abstract: 
  

  Seven-membered ring mimetics of mannose were studied as ligands for the mannose-specific bacterial lectin FimH, which plays an essential role in the first step of urinary tract infections (UTI). A competitive binding assay and isothermal titration calorimetry (ITC) experiments indicated an approximately ten-fold lower affinity for the seven-membered ring mannose mimetic 2- O-n -heptyl-1,6-anhydro-d- glycero -d-galactitol ( 7 ) compared to n -heptyl α-d-mannopyranoside ( 2 ), resulting exclusively from a loss of conformational entropy. Investigations by solution NMR, X-ray crystallography, and molecular modeling revealed that 7 establishes a superimposable H-bond network compared to mannoside 2 , but at the price of a high entropic penalty due to the loss of its pronounced conformational flexibility. These results underscore the importance of having access to the complete thermodynamic profile of a molecular interaction to "rescue" ligands from entropic penalties with an otherwise perfect fit to the protein binding site.

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Organizational Affiliation: 
• University of Basel , Institute of Molecular Pharmacy , Pharmacenter of the University of Basel , Klingelbergstrasse 50 , 4056 , Basel , Switzerland . Email: [e-mail].
Department of Chemistry , University of Connecticut , 55 N. Eagleville Road U3060, Storrs , CT , 06279 USA . Email: [e-mail].
University of Basel , Biozentrum: Focal Area Structural Biology , Klingelbergstrasse 70 , 4056 Basel , Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.61 kDa 
• Atom Count: 2,923 
• Modeled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein FimH	A, B	158	Escherichia coli K-12	Mutation(s): 0  Gene Names: fimH, b4320, JW4283
UniProt
Find proteins for P08191 (Escherichia coli (strain K12)) Explore P08191  Go to UniProtKB:  P08191

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
51C	C [auth A], E [auth B]	(6R)-1,6-anhydro-2-O-heptyl-6-(hydroxymethyl)-D-galactitol C14 H28 O6 WXAPBESCSQWOGD-ITGHMWBKSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
51C	BindingDB:  5CGB	Kd: 3.18e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.58	α = 90
b = 68.55	β = 90
c = 95.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Jakob, R.P., Preston, R.P., Zihlmann, P., Fiege, B., Sager, C.P., Vannam, R., Rabbani, S., Zalewski, A., Maier, T., Ernst, B., Peczuh, M.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary