9S9E | pdb_00009s9e

Co-crystal of broadly neutralizing biparatopic monomeric VHH in complex with cardiotoxin (P01468) naja pallida

• PDB DOI: https://doi.org/10.2210/pdb9S9E/pdb
• Entry: 9S9E supersedes: 9RIT

• Classification: ANTITOXIN
• Organism(s): Vicugna pacos, Naja pallida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-06 Released: 2026-09-02 
• Deposition Author(s): Burlet, N.J., Laustsen, A.H., Morth, J.P.
• Funding Organization(s): European Research Council (ERC), Wellcome Trust, Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: in silico

Literature

Structural and functional characterization of a biparatopic monomeric nanobody

Burlet, N.J., Yildirim, E.B., Tomberli, I., Bertelsen, A.B., Ahmadi, S., Ljungars, A., Laustsen, A.H., Morth, J.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 41.58 kDa 
• Atom Count: 3,126 
• Modeled Residue Count: 356 
• Deposited Residue Count: 370 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable Domain of Heavy-Chain only Antibody (VHH) TPL0870_01_G09_Wt	A, B	125	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxin 1	C, D	60	Naja pallida	Mutation(s): 0
UniProt
Find proteins for P01468 (Naja pallida) Explore P01468  Go to UniProtKB:  P01468

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], F [auth A], G [auth B], H [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.934	α = 90
b = 54.826	β = 90
c = 143.062	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-02 
Deposition Author(s): Burlet, N.J., Laustsen, A.H., Morth, J.P.
• This entry supersedes: 9RIT

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	850974
Wellcome Trust	United Kingdom	221702/Z/20/Z
Novo Nordisk Foundation	Denmark	NNF24OC0088714

Revision History  

• Version 1.0: 2026-09-02
  Type: Initial release