5XWE | pdb_00005xwe

Structure of a three finger toxin from Ophiophagus hannah venom

• PDB DOI: https://doi.org/10.2210/pdb5XWE/pdb

• Classification: TOXIN
• Organism(s): Ophiophagus hannah
• Mutation(s): No 


• Deposited: 2017-06-29 Released: 2018-07-11 
• Deposition Author(s): Jobichen, C., Roy, A., Kini, R.M., Sivaraman, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Starting Model: experimental

Literature

Structure of a three finger toxin from Ophiophagus hannah venom

Jobichen, C., Roy, A., Kin, R.M., Sivaraman, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 19.22 kDa 
• Atom Count: 849 
• Modeled Residue Count: 101 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Weak toxin DE-1 homolog 1	A, B	83	Ophiophagus hannah	Mutation(s): 0
UniProt
Find proteins for Q69CJ8 (Ophiophagus hannah) Explore Q69CJ8  Go to UniProtKB:  Q69CJ8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.48	α = 90
b = 18.183	β = 104.75
c = 77.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Jobichen, C., Roy, A., Kini, R.M., Sivaraman, J.

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 2.0: 2021-06-02
  Type: Coordinate replacement
  Reason: Atoms with unrealistic or zero occupancies
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary