PDBsum entry 1cod

Short neurotoxin

PDB id: 1cod

Contents

Protein chain

62 a.a. *

* Residue conservation analysis

PDB id:

1cod

Name:

Short neurotoxin

Title:

Solution conformation of cobrotoxin: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study

Structure:

Cobrotoxin. Chain: a. Engineered: yes

Source:

Naja atra. Chinese cobra. Organism_taxid: 8656. Tissue: venom

NMR struc:

1 models

Authors:

C.Yu,R.Bhaskaran,C.C.Yang

Key ref:

C.Yu et al. (1993). Solution conformation of cobrotoxin: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study. Biochemistry, 32, 2131-2136. PubMed id: 8443154 DOI: 10.1021/bi00060a002

Date:

11-May-94 Release date: 26-Jan-95

Protein chain

Q9PTT0  (3S1CB_NAJNA) -  Cobrotoxin homolog from Naja naja

Seq: 83 a.a.

Struc: 62 a.a.

DOI no: 10.1021/bi00060a002

Biochemistry 32:2131-2136 (1993)

PubMed id: 8443154

Solution conformation of cobrotoxin: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study.

C.Yu, R.Bhaskaran, L.C.Chuang, C.C.Yang.

ABSTRACT

The solution conformation of cobrotoxin has been determined by using proton nuclear magnetic resonance spectroscopy. With the combination of various two-dimensional NMR techniques, the 1H-NMR spectrum of cobrotoxin was completely assigned (Yu et al., 1990). A set of 435 approximate interproton distance restraints was derived from nuclear Overhauser enhancement (NOE) measurements. These NOE constraints, in addition to the 29 dihedral angle constraints (from coupling constant measurements) and 26 hydrogen bonding restraints (from the pattern of short-range NOEs), form the basis of 3-D structure determination by the hybrid distance geometry-dynamical simulated annealing method. The 23 structures that were obtained satisfy the experimental restraints, display small deviation from idealized covalent geometry, and possess good nonbonded contacts. Analysis of converged structures indicated that there are two antiparallel beta sheets (double and triple stranded), duly confirming our earlier observations. These are well defined in terms of both atomic root mean square (RMS) differences and backbone torsional angles. The average backbone RMS deviation between the calculated structures and the mean structure, for the beta-sheet regions, is 0.92 A. The mean solution structure was compared with the X-ray crystal structure of erabutoxin b, the homologous protein. This yielded information that both structures resemble each other except at the exposed loop/surface regions, where the solution structure seems to possess more flexibility.