1H8S

Three-dimensional structure of anti-ampicillin single chain Fv fragment complexed with the hapten.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Selection, Characterization and X-Ray Structure of Anti-Ampicillin Single-Chain Fv Fragments from Phage-Displayed Murine Antibody Libraries

Burmester, J.Spinelli, S.Pugliese, L.Krebber, A.Honegger, A.Jung, S.Schimmele, B.Cambillau, C.Pluckthun, A.

(2001) J.Mol.Biol. 309: 671

  • DOI: 10.1006/jmbi.2001.4663
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Single-chain Fv (scFv) antibody libraries were constructed from mice immunized with an ampicillin-bovine serum albumin conjugate. Several antibodies with specificity for intact ampicillin were selected by phage display and characterized. The antibody ...

    Single-chain Fv (scFv) antibody libraries were constructed from mice immunized with an ampicillin-bovine serum albumin conjugate. Several antibodies with specificity for intact ampicillin were selected by phage display and characterized. The antibody scFv fragment aL2 binds to intact ampicillin and shows no detectable cross-reactivity with hydrolyzed ampicillin. We determined the X-ray structures of two crystal forms of w.t. aL2, which differ mainly in the side-chain conformation of Trp H109 (according to a new consensus nomenclature Kabat residue number H95) in the extremely short (three residues) CDR H3 and the presence or absence of a well-resolved molecule of 2-methyl-pentane-2,4-diol in the bottom of the binding pocket. Attempts to co-crystallize aL2 with its antigen or to diffuse ampicillin into the wild-type aL2 crystals were unsuccessful, since crystal contacts obstruct the binding pocket. However, a mutant with two point mutations near the N terminus (Gln H6 replaced by Glu and Ala H10 (Kabat H9) replaced by Gly) crystallized in a form compatible with antigen-binding. Although the mutations affect the conformation of framework I, the conformations of the binding pocket of the uncomplexed wild-type aL2 and of the mutant complex were almost identical. The structure explains the specificity of the antibody for intact ampicillin and the degree of cross-reactivity of aL2 with a wide variety of ampicillin analogs. This antibody system will be very useful as a diagnostic reagent for antibiotics use and abuse, as a model for the effect of expression of antibiotic binding molecules in Escherichia coli, and for directed evolution towards high antibiotic resistance.


    Organizational Affiliation

    Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MUTANT AL2 6E7P9G
A, B
252N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AIC
Query on AIC

Download SDF File 
Download CCD File 
A
(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
AMPICILLIN; D(-)-ALPHA-AMINOBENZYLPENICILLIN; 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID
C16 H19 N3 O4 S
AVKUERGKIZMTKX-NJBDSQKTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AICKd: 1540 nM BINDINGMOAD
AICKd: 1540 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.930α = 90.00
b = 89.270β = 90.00
c = 94.410γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-02
    Type: Initial release