1IND

HOW THE ANTI-(METAL CHELATE) ANTIBODY CHA255 IS SPECIFIC FOR THE METAL ION OF ITS ANTIGEN: X-RAY STRUCTURES FOR TWO FAB'(SLASH)HAPTEN COMPLEXES WITH DIFFERENT METALS IN THE CHELATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

How the anti-(metal chelate) antibody CHA255 is specific for the metal ion of its antigen: X-ray structures for two Fab'/hapten complexes with different metals in the chelate.

Love, R.A.Villafranca, J.E.Aust, R.M.Nakamura, K.K.Jue, R.A.Major Jr., J.G.Radhakrishnan, R.Butler, W.F.

(1993) Biochemistry 32: 10950-10959

  • DOI: https://doi.org/10.1021/bi00092a004
  • Primary Citation of Related Structures:  
    1IND, 1INE

  • PubMed Abstract: 

    Antibodies with bound metal-chelate haptens provide new means for exploiting the diverse properties of metallic elements. The murine monoclonal antibody CHA255 (IgG1 lambda) binds the metal-chelate hapten indium (III)-4-[N'-(2-hydroxyethyl)thioureido]-L-benzyl-EDTA (designated In-EOTUBE) with high affinity (K(a) = 1.1 x 10(10) M-1). Antibody binding is highly specific for the indium chelate; the affinity decreases as much as 10(4) with other metals, even those having ionic radii close to indium. To better understand this selectivity, the crystal structure of the antigen-binding fragment (Fab') of CHA255 complexed with its hapten, In(III)-EOTUBE, was determined by molecular replacement and refined at 2.2-A resolution. The structure of CHA255 Fab' complexed with Fe(III)-EOTUBE was also determined and refined at 2.8-A resolution. In both structures, the hapten's EDTA moiety is half-buried near the center of the complementarity-determining regions (CDR's). Five of the six CDR's on the Fab' interact with the hapten through protein side-chain atoms (but not main-chain atoms). A novel feature of the In-EOTUBE/Fab' complex is coordination of the indium by N epsilon of one histidine from the heavy chain's third CDR (distance = 2.4 A). The histidine coordination is not observed in the Fe-EOTUBE/Fab' complex, due mainly to a slightly different hapten conformation that reduces metal accessibility; this may partially explain the 20-fold lower affinity of CHA255 for iron hapten. An unexpected feature of the Fab' overall is an elbow angle of 193 degrees (the angle between the pseudodyad axes of the Fab's constant and variable domains).


  • Organizational Affiliation

    Agouron Pharmaceuticals, Inc., San Diego, California 92121.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IGG1-LAMBDA CHA255 FAB (LIGHT CHAIN)A [auth L]215Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IGG1-LAMBDA CHA255 FAB (HEAVY CHAIN)B [auth H]226Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EOT
Query on EOT

Download Ideal Coordinates CCD File 
D [auth H][(1-[(BIS-CARBOXYMETHYL-AMINO)-METHYL]-2-{4-[3-(2-HYDROXY-ETHYL)-THIOUREIDO]-PHENY}-ETHYL)-CARBOXYMETHYL-AMINO]-ACETIC ACID
C20 H28 N4 O9 S
PQYGLZAKNWQTCV-HNNXBMFYSA-N
IN
Query on IN

Download Ideal Coordinates CCD File 
C [auth H]INDIUM (III) ION
In
RJMMFJHMVBOLGY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth L]L-PEPTIDE LINKINGC5 H7 N O3GLN
Binding Affinity Annotations 
IDSourceBinding Affinity
EOT PDBBind:  1IND Kd: 0.09 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.3α = 90
b = 84.6β = 136.2
c = 76.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 2.0: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Polymer sequence, Structure summary