PDBsum entry 1sb2

Toxin

PDB id: 1sb2

Contents

Protein chains

132 a.a. *

124 a.a. *

Waters ×167

* Residue conservation analysis

PDB id:

1sb2

Name:

Toxin

Title:

High resolution structure determination of rhodocetin

Structure:

Rhodocetin alpha subunit. Chain: a. Rhodocetin beta subunit. Chain: b

Source:

Calloselasma rhodostoma. Malayan pit viper. Organism_taxid: 8717. Other_details: organism name synonym: agkistrodon rhodostoma. Other_details: organism name synonym: agkistrodon rhodostoma

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.191 R-free: 0.231

Authors:

P.Paaventhan,C.G.Kong,J.S.Joseph,M.C.M.Chung,P.R.Kolatkar

Key ref:

P.Paaventhan et al. (2005). Structure of rhodocetin reveals noncovalently bound heterodimer interface. Protein Sci, 14, 169-175. PubMed id: 15576563 DOI: 10.1110/ps.04945605

Date:

10-Feb-04 Release date: 01-Feb-05

Protein chain

P81397  (SLEA_CALRH) -  Snaclec rhodocetin subunit alpha from Calloselasma rhodostoma

Seq: 133 a.a.

Struc: 132 a.a.

Protein chain

P81398  (SLEB_CALRH) -  Snaclec rhodocetin subunit beta from Calloselasma rhodostoma

Seq: 129 a.a.

Struc: 124 a.a.

DOI no: 10.1110/ps.04945605

Protein Sci 14:169-175 (2005)

PubMed id: 15576563

Structure of rhodocetin reveals noncovalently bound heterodimer interface.

P.Paaventhan, C.Kong, J.S.Joseph, M.C.Chung, P.R.Kolatkar.

ABSTRACT

Rhodocetin is a unique heterodimer consisting of alpha- and beta-subunits of 133 and 129 residues, respectively. The molecule, purified from the crude venom of the Malayan pit viper, Calloselasma rhodostoma, functions as an inhibitor of collagen-induced aggregation. Rhodocetin has been shown to have activity only when present as a dimer. The dimer is formed without an intersubunit disulfide bridge, unlike all the other Ca(2+)-dependent lectin-like proteins. We report here the 1.9 A resolution structure of rhodocetin, which reveals the compensatory interactions that occur in the absence of the disulfide bridge to preserve activity.

Selected figure(s)

Figure 4.
Figure 4. Superposition of subunits A in IX/X-bp (red), IX-bp (green), and botrocetin (yellow) with rhodocetin -subunit (blue) shows that the loop in rhodocetin spanning 27 residues is rotated by ~90° with respect to the similar loop in IX/X-bp.

Figure 7.
Figure 7. Geometry around the Ca^2+-binding site in CLPs. (A) Subunit A. (B) Subunit B. Superposition of the Ca^2+ ion coordination site in IX/X-bp (green) with the corresponding site in rhodocetin (blue). Glu 128A and Glu 120B of IX/X-bp are replaced by Lys 128 in the -subunit and Lys 124 in the -subunit, respectively. This substitution could prevent the metal ion from binding rhodocetin.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 169-175) copyright 2005.

Figures were selected by an automated process.