1ZEA

Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of an anti-cholera toxin antibody Fab in complex with an epitope-derived D-peptide: a case of polyspecific recognition.

Scheerer, P.Kramer, A.Otte, L.Seifert, M.Wessner, H.Scholz, C.Krauss, N.Schneider-Mergener, J.Hohne, W.

(2007) J.Mol.Recognit. 20: 263-274

  • DOI: 10.1002/jmr.838

  • PubMed Abstract: 
  • The structure of a complex of the anti-cholera toxin antibody TE33 Fab (fragment antibody) with the D-peptide vpGsqhyds was solved to 1.78 A resolution. The D-peptide was derived from the linear L-peptide epitope VPGSQHIDS by a stepwise transformatio ...

    The structure of a complex of the anti-cholera toxin antibody TE33 Fab (fragment antibody) with the D-peptide vpGsqhyds was solved to 1.78 A resolution. The D-peptide was derived from the linear L-peptide epitope VPGSQHIDS by a stepwise transformation. Despite the very similar amino acid sequence-the only difference is a tyrosine residue in position 7-there are marked differences in the individual positions with respect to their contribution to the peptide overall affinity as ascertained by a complete substitutional analysis. This is reflected by the X-ray structure of the TE33 Fab/D-peptide complex where there is an inverted orientation of the D-peptide as compared with the known structure of a corresponding complex containing the epitope L-peptide, with the side chains establishing different contacts within the binding site of TE33. The D- and L-peptide affinities are comparable and the surface areas buried by complex formation are almost the same. Thus the antibody TE33 provides a typical example for polyspecific binding behavior of IgG family antibodies.


    Organizational Affiliation

    Charité-Universitätsmedizin Berlin, Institute of Biochemistry, Monbijoustr. 2, D-10117 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
monoclonal anti-cholera toxin IGG1 KAPPA antibody, L chain
L
216Mus musculusMutation(s): 0 
Gene Names: Igkc (Igk-C)
Find proteins for A2NHM3 (Mus musculus)
Go to UniProtKB:  A2NHM3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
monoclonal anti-cholera toxin IGG1 KAPPA antibody, H chain
H
216Mus musculusMutation(s): 0 
Find proteins for Q921A6 (Mus musculus)
Go to UniProtKB:  Q921A6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
short synthetic D-amino acid peptide D2
A
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
L
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  7 Unique
IDChainsTypeFormula2D DiagramParent
DPR
Query on DPR
A
D-PEPTIDE LINKINGC5 H9 N O2

--

DHI
Query on DHI
A
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DSN
Query on DSN
A
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
A
D-PEPTIDE LINKINGC5 H11 N O2

--

DGN
Query on DGN
A
D-PEPTIDE LINKINGC5 H10 N2 O3

--

DAS
Query on DAS
A
D-PEPTIDE LINKINGC4 H7 N O4

--

DTY
Query on DTY
A
D-PEPTIDE LINKINGC9 H11 N O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.638α = 90.00
b = 108.862β = 90.00
c = 40.210γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-08-28
    Type: Data collection, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-10-16
    Type: Data collection