8R4N | pdb_00008r4n

Crystal structure of neutralizing Fab Eq4.Dp46-3A from equine antivenom bound to short chain three finger alpha-neurotoxin from Dendroaspis polylepis.

• PDB DOI: https://doi.org/10.2210/pdb8R4N/pdb

• Classification: ANTITOXIN
• Organism(s): Equus caballus, Dendroaspis polylepis
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2023-11-14 Released: 2025-05-28 
• Deposition Author(s): Wibmer, C.K.
• Funding Organization(s): National Institutes of Health/John E. Fogarty International Center (NIH/FIC), Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Models: experimental

Literature

A monoclonal antibody from horses that neutralizes long and short chain three finger neurotoxins

Wibmer, C.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.49 kDa 
• Atom Count: 3,750 
• Modeled Residue Count: 488 
• Deposited Residue Count: 520 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eq4.Dp46-3A heavy chain	A [auth H]	236	Equus caballus	Mutation(s): 0  Gene Names: IgHV

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Eq4.Dp46-3A lambda chain	B [auth L]	217	Equus caballus	Mutation(s): 0  Gene Names: IgHV

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Short neurotoxin 1	C [auth N]	67	Dendroaspis polylepis	Mutation(s): 0
UniProt
Find proteins for P01416 (Dendroaspis polylepis polylepis) Explore P01416  Go to UniProtKB:  P01416

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.623	α = 90
b = 104.623	β = 90
c = 216.427	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2.multiplex	data reduction
xia2.multiplex	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Wibmer, C.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)	United States	5R21TW011454-02
Royal Society	United Kingdom	FLR-R1-201782

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release