PDBsum entry 2c1p

Immune system

PDB id: 2c1p

Contents

Protein chains

218 a.a.

217 a.a. *

Ligands

FNZ ×2

Waters ×429

* Residue conservation analysis

PDB id:

2c1p

Name:

Immune system

Title:

Fab-fragment of enantioselective antibody complexed with finrozole

Structure:

Igk-c protein. Chain: a, l. Synonym: finrozole-binding antibody. Engineered: yes. Igh-4 protein. Chain: b, h. Fragment: fab-fragment. Synonym: finrozole-binding antibody. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.230 R-free: 0.285

Authors:

T.Parkkinen,T.K.Nevanen,A.Koivula,J.Rouvinen

Key ref:

T.Parkkinen et al. (2006). Crystal structures of an enantioselective fab-fragment in free and complex forms. J Mol Biol, 357, 471-480. PubMed id: 16427081 DOI: 10.1016/j.jmb.2005.12.045

Date:

19-Sep-05 Release date: 25-Jan-06

Protein chains

Q58EU8  (Q58EU8_MOUSE) -  Igk protein from Mus musculus

Seq: 239 a.a.

Struc: 218 a.a.*

Protein chains

No UniProt id for this chain

Struc: 217 a.a.

* PDB and UniProt seqs differ at 15 residue positions (black crosses)

DOI no: 10.1016/j.jmb.2005.12.045

J Mol Biol 357:471-480 (2006)

PubMed id: 16427081

Crystal structures of an enantioselective fab-fragment in free and complex forms.

T.Parkkinen, T.K.Nevanen, A.Koivula, J.Rouvinen.

ABSTRACT

Enantioselective antibodies can separate the enantiomers of a chiral compound in a highly specific manner. We have recently reported the cloning and applications of a recombinant Fab-fragment, ENA11His, in the enantioseparation of a drug candidate, finrozole, which contains two chiral centers. Here, the crystal structures of this enantioselective antibody Fab-fragment are determined in the absence of the hapten at a resolution of 2.75 A, and in the presence of the hapten at 2.05 A resolution. The conformation of the protein was found to be similar in both free and complex forms. The hapten molecule was tightly bound in a deep cleft between the light and heavy chains of the Fab-fragment. The complex structure also allowed us to describe the molecular basis for enantioselectivity and to deduce the absolute configurations of all the four different stereoisomers (a-d) of finrozole. The ENA11His antibody fragment selectively binds the SR (a) enantiomer from the racemic mixture of a and d-enantiomers, thus allowing separation from the pharmacologically most active RS enantiomer (d). In particular, Asp95 and Asn35 of the H-chain in the ENA11 His antibody seem to provide this specificity through hydrogen bonding.

Selected figure(s)

Figure 2.
Figure 2. Comparison of the inhibition effect of the soluble stereoisomers a, b, c, and d on the binding of ENA11His to the ad-BSA surface of a BIAcore sensor chip. The a and b stereoisomers show the strongest inhibition effect by lowering the binding response the most. DMSO is a control, as described in the text.

Figure 4.
Figure 4. A stereo view of the electron density map of the a-enantiomer in the ENA11His Fab binding site at 2.05 Å resolution. The F[o] -F[c] omit map is contoured at 3s. The electron density clearly shows that only the SR configuration is bound into the binding site.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 471-480) copyright 2006.

Figures were selected by an automated process.