1MD2

CHOLERA TOXIN B-PENTAMER WITH DECAVALENT LIGAND BMSC-0013


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Solution and crystallographic studies of branched multivalent ligands that inhibit the receptor-binding of cholera toxin.

Zhang, Z.Merritt, E.A.Ahn, M.Roach, C.Hou, Z.Verlinde, C.L.Hol, W.G.Fan, E.

(2002) J.Am.Chem.Soc. 124: 12991-12998


  • PubMed Abstract: 
  • The structure-based design of multivalent ligands offers an attractive strategy toward high affinity protein inhibitors. The spatial arrangement of the receptor-binding sites of cholera toxin, the causative agent of the severe diarrheal disease chole ...

    The structure-based design of multivalent ligands offers an attractive strategy toward high affinity protein inhibitors. The spatial arrangement of the receptor-binding sites of cholera toxin, the causative agent of the severe diarrheal disease cholera and a member of the AB(5) bacterial toxin family, provides the opportunity of designing branched multivalent ligands with 5-fold symmetry. Our modular synthesis enabled the construction of a family of complex ligands with five flexible arms each ending with a bivalent ligand. The largest of these ligands has a molecular weight of 10.6 kDa. These ligands are capable of simultaneously binding to two toxin B pentamer molecules with high affinity, thus blocking the receptor-binding process of cholera toxin. A more than million-fold improvement over the monovalent ligand in inhibitory power was achieved with the best branched decavalent ligand. This is better than the improvement observed earlier for the corresponding nonbranched pentavalent ligand. Dynamic light scattering studies demonstrate the formation of concentration-dependent unique 1:1 and 1:2 ligand/toxin complexes in solution with no sign of nonspecific aggregation. This is in complete agreement with a crystal structure of the branched multivalent ligand/toxin B pentamer complex solved at 1.45 A resolution that shows the specific 1:2 ligand/toxin complex formation in the solid state. These results reiterate the power of the structure-based design of multivalent protein ligands as a general strategy for achieving high affinity and potent inhibition.


    Organizational Affiliation

    Biomolecular Structure Center and Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHOLERA TOXIN B SUBUNIT
D, E, F, G, H
103Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Gene Names: ctxB (toxB)
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  P01556
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
F
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
233
Query on 233

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Download CCD File 
D, E, F
[5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLCARBAMOYL)-PENTYL]-CARBAMIC ACID METHYL ESTER
BMSC-0013
C14 H26 N2 O8
YTYAKGJMNHDUDF-UUWLPUTASA-N
 Ligand Interaction
SQ
Query on SQ

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Download CCD File 
D, E
3-ETHYLAMINO-4-METHYLAMINO-CYCLOBUTANE-1,2-DIONE
SQUARIC ACID
C7 H12 N2 O2
FYAIPBIOBLLUAM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
D, E, F, G, H
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
233Kd: ~40 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.125 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.124α = 90.00
b = 66.176β = 106.33
c = 78.221γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
TRUNCATEdata reduction
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description