9FYS | pdb_00009fys

D11 mAbs bound to alpha-Bungarotoxin

• PDB DOI: https://doi.org/10.2210/pdb9FYS/pdb

• Classification: TOXIN
• Organism(s): Homo sapiens, Bungarus multicinctus
• Expression System: Escherichia coli, Bungarus multicinctus
• Mutation(s): No 


• Deposited: 2024-07-03 Released: 2025-07-16 
• Deposition Author(s): Wade, J., Bohn, M.F., Laustsen, A.H., Morth, J.P.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.192 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: in silico

Literature

Structural mechanisms of a-neurotoxin-neutralizing antibodies enable rational design of pH-dependent antigen binding

Wade, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Macromolecule Content 

• Total Structure Weight: 77.31 kDa 
• Atom Count: 5,926 
• Modeled Residue Count: 651 
• Deposited Residue Count: 720 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain	A [auth C], E [auth M]	121	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-bungarotoxin	B [auth X], C [auth Z]	95	Bungarus multicinctus	Mutation(s): 0
UniProt
Find proteins for P60615 (Bungarus multicinctus) Explore P60615  Go to UniProtKB:  P60615

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
D11 mAbs Light chain	D [auth I], F [auth B]	144	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	G [auth Z]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.192 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.847	α = 90
b = 83.804	β = 90
c = 102.779	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Wade, J., Bohn, M.F., Laustsen, A.H., Morth, J.P.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release