PDBsum entry 1jhk

Immune system

PDB id: 1jhk

Contents

Protein chains

213 a.a. *

205 a.a. *

Waters ×162

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of a recombinant anti-Estradiol FAB fragment in complex with 17beta -Estradiol.

Authors

U.Lamminmäki, J.A.Kankare.

Ref.

J Biol Chem, 2001, 276, 36687-36694. [DOI no: 10.1074/jbc.M102367200]

PubMed id

11451948

Abstract

The crystal structure of a Fab fragment of an anti-17beta-estradiol antibody 57-2 was determined in the absence and presence of the steroid ligand, 17beta-estradiol (E2), at 2.5 and 2.15-A resolutions, respectively. The antibody binds the steroid in a deep hydrophobic pocket formed at the interface between the variable domains. No major structural rearrangements take place upon ligand binding; however, a large part of the heavy chain variable domain near the binding pocket is unusually flexible and is partly stabilized when the steroid is bound. The nonpolar steroid skeleton of E2 is recognized by a number of hydrophobic interactions, whereas the two hydroxyl groups of E2 are hydrogen-bonded to the protein. Especially, the 17-hydroxyl group of E2 is recognized by an intricate hydrogen bonding network in which the 17-hydroxyl itself forms a rare four-center hydrogen bond with three polar amino acids; this hydrogen bonding arrangement accounts for the low cross-reactivity of the antibody with other estrogens such as estrone. The CDRH3 loop plays a prominent role in ligand binding. All the complementarity-determining regions of the light chain make direct contacts with the steroid, even CDRL2, which is rarely directly involved in the binding of haptens.

Figure 4.
Fig. 4. A A-weighted (2F[o] F[c]) exp(i [calc]) electron density omit map of the ligand binding site contoured at 1 and shown in stereo. The steroid atoms are shown as a black ball-and-stick model. The steroid atoms were omitted from the map calculation.

Figure 7.
Fig. 7. A close-up of Fig. 6A with three steroid analogs superimposed on E2. The coloring is as in Fig. 6A, but the carbon atoms of the E2 analogs are colored as follows: E1 is yellow, 17 -estradiol ( ) is brown, and E3 is purple. The 17-hydroxyl-keto groups of the steroids are labeled with the name of the corresponding steroid. In addition, the 16-hydroxyl of E3 is labeled.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 36687-36694) copyright 2001.

Secondary reference #1

Title

Crystallization and preliminary X-Ray analysis of a recombinant FAB fragment in complex with 17beta-Oestradiol.

Authors

U.Lamminmäki, J.Kankare.

Ref.

Acta Crystallogr D Biol Crystallogr, 2000, 56, 1670-1672. [DOI no: 10.1107/S0907444900013317]

PubMed id

11092942

Figure 1.
Figure 1 Apo-form crystals of the Fab fragment of anti-oestradiol antibody 57-2 obtained with microseeding. The dimensions of the largest crystal are approximately 0.6 × 0.3 × 0.1 mm.

The above figure is reproduced from the cited reference with permission from the IUCr