1SB2

High resolution Structure determination of rhodocetin

• PDB DOI: https://doi.org/10.2210/pdb1SB2/pdb

• Classification: TOXIN
• Organism(s): Calloselasma rhodostoma
• Mutation(s): No 


• Deposited: 2004-02-10 Released: 2005-02-01 
• Deposition Author(s): Paaventhan, P., Kong, C.G., Joseph, J.S., Chung, M.C.M., Kolatkar, P.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.231 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Structure of rhodocetin reveals noncovalently bound heterodimer interface

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

(2005) Protein Sci 14: 169-175

• PubMed: 15576563 
• DOI: https://doi.org/10.1110/ps.04945605
• Primary Citation of Related Structures:  
  1SB2


• PubMed 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.

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Organizational Affiliation: 

Genome Institute of Singapore, Singapore 138672.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.2 kDa 
• Atom Count: 2,271 
• Modelled Residue Count: 256 
• Deposited Residue Count: 262 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodocetin alpha subunit	A	133	Calloselasma rhodostoma	Mutation(s): 0
UniProt
Find proteins for P81397 (Calloselasma rhodostoma) Explore P81397  Go to UniProtKB:  P81397

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodocetin beta subunit	B	129	Calloselasma rhodostoma	Mutation(s): 0
UniProt
Find proteins for P81398 (Calloselasma rhodostoma) Explore P81398  Go to UniProtKB:  P81398

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.231 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.875	α = 90
b = 65.935	β = 90
c = 118.841	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Paaventhan, P., Kong, C.G., Joseph, J.S., Chung, M.C.M., Kolatkar, P.R.

Revision History  

• Version 1.0: 2005-02-01
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance