PDBsum entry 1q0x

Immune system

PDB id: 1q0x

Contents

Protein chains

212 a.a. *

215 a.a. *

Ligands

SO4 ×2

PG4

Waters ×327

* Residue conservation analysis

PDB id:

1q0x

Name:

Immune system

Title:

Anti-morphine antibody 9b1 unliganded form

Structure:

Fab 9b1, light chain. Chain: l. Fab 9b1, heavy chain. Chain: h. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.216 R-free: 0.251

Authors:

E.Pozharski,M.A.Wilson,A.Hewagama,A.B.Shanafelt,G.Petsko,D.Ringe

Key ref:

E.Pozharski et al. (2004). Anchoring a cationic ligand: the structure of the Fab fragment of the anti-morphine antibody 9B1 and its complex with morphine. J Mol Biol, 337, 691-697. PubMed id: 15019787 DOI: 10.1016/j.jmb.2003.12.084

Date:

17-Jul-03 Release date: 20-Apr-04

Protein chain

P01723  (LV1A_MOUSE) -  Ig lambda-1 chain V region from Mus musculus

Seq: 117 a.a.

Struc: 212 a.a.*

Protein chain

Q9D9B8  (Q9D9B8_MOUSE) -  Ig-like domain-containing protein from Mus musculus

Seq: 111 a.a.

Struc: 215 a.a.*

* PDB and UniProt seqs differ at 30 residue positions (black crosses)

DOI no: 10.1016/j.jmb.2003.12.084

J Mol Biol 337:691-697 (2004)

PubMed id: 15019787

Anchoring a cationic ligand: the structure of the Fab fragment of the anti-morphine antibody 9B1 and its complex with morphine.

E.Pozharski, M.A.Wilson, A.Hewagama, A.B.Shanafelt, G.Petsko, D.Ringe.

ABSTRACT

The crystal structures of an anti-morphine antibody 9B1 (to 1.6A resolution) and its complex with morphine (to 2.0 A resolution) are reported. The morphine-binding site is described as a shallow depression on the protein surface, an unusual topology for a high-affinity ( Ka approximately 10(9) M(-1)) antibody against a small antigen. The polar part of the ligand is exposed to solvent, and the cationic nitrogen atom of the morphine molecule is anchored at the bottom of the binding site by a salt-bridge to a glutamate side-chain. Additional affinity is provided by a double cation-pi interaction with two tryptophan residues. Comparison of the morphine complex with the structure of the free Fab shows that a domain closure occurs upon binding of the ligand.

Selected figure(s)

Figure 2.
Figure 2. Stereo view of the morphine-binding site. Shown are nine residues forming a contact surface for the ligand.

Figure 3.
Figure 3. A drawing of the binding site. A, Cation-p interaction of the morphine amine and the aromatic side-chains of TrpL91 and TrpH95. B, The salt-bridge between the morphine nitrogen atom and the carboxylate group of GluH50. C, Hydrogen bonding network around the GluH50 side-chain. D, The water molecule in the hapten-binding pocket.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 691-697) copyright 2004.

Figures were selected by an automated process.