1DBA

THREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex.

Arevalo, J.H., Stura, E.A., Taussig, M.J., Wilson, I.A.

(1993) J.Mol.Biol. 231: 103-118

  • DOI: 10.1006/jmbi.1993.1260
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progest ...

    The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progesterone-like steroids. Crystals of the unliganded Fab' and various steroid-Fab' complexes are isomorphous and belong to the hexagonal space group, P6(4)22, with unit cell dimensions of a = b = 135 A, c = 124 A. Structures of free and progesterone-bound Fab' have been determined by X-ray crystallography at 2.7 A resolution using molecular replacement techniques. Progesterone is bound in a hydrophobic pocket formed mainly by the interaction of three complementarity determining regions L1, H2 and H3. The orientation of the ligand in the binding site was aided by both crystallographic and biochemical analyses of substituted steroids. The indole side-chain of TrpH100 of the DB3 has two different conformations, inter-converting "open" and "closed" forms of the antibody combining site. The TrpH100 indole thus appears to be acting as an antibody-derived surrogate ligand for its own hydrophobic binding pocket. These structures provide the first atomic view of how a steroid interacts with a protein and offer a structural explanation for the restriction of the anti-progesterone response to the VGAM3.8 family of VH genes.

    Related Citations: 
    • Analysis of an Anti-Progesterone Antibody: Variable Crystal Morphology of the Fab' and Steroid-Fab' Complexes
      Stura, E.A.,Arevalo, J.H.,Feinstein, A.,Heap, R.B.,Taussig, M.J.,Wilson, I.A.
      (1987) Immunology 62: 511

    Organizational Affiliation: 

    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA DB3 FAB (LIGHT CHAIN)
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA DB3 FAB (HEAVY CHAIN)
H
219Mus musculusMutation(s): 0 
Gene Names: Ighg1 (Igh-4)
Find proteins for P01868 (Mus musculus)
Go to UniProtKB:  P01868
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EOH
Query on EOH
Download SDF File 
Download CCD File 
H
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.202 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 134.760α = 90.00
b = 134.760β = 90.00
c = 124.210γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance