8V13

Crystal structure of Black mamba toxin in complex with Centi-SNX-B03 antibody

• PDB DOI: https://doi.org/10.2210/pdb8V13/pdb

• Classification: ANTITOXIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Dendraspis polylepis polylepis
• Expression System: Homo sapiens, Dendraspis polylepis polylepis
• Mutation(s): No 


• Deposited: 2023-11-19 Released: 2025-01-29 
• Deposition Author(s): Pletnev, S., Glanville, J., Kwong, P.D.
• Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: in silico

Literature

Venom protection by broadly neutralizing antibody from a snakebite subject

Glanville, J., Andrade, J., Bellin, M., Kim, S., Pletnev, S., Tsao, D., Verardi, R., Bedi, R., Friede, T., Tully, E., Zhang, B., Bylund, T., Liu, T., Kwong, P.D.

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 PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.83 kDa 
• Atom Count: 8,271 
• Modelled Residue Count: 991 
• Deposited Residue Count: 1,010 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centi-SNX-B03 Fab heavy chain	A [auth H], D [auth h]	230	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Centi-SNX-B03 Fab light chain	B [auth L], E [auth l]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Short neurotoxin 1	C [auth T], F [auth t]	60	Dendraspis polylepis polylepis	Mutation(s): 0
UniProt
Find proteins for P01416 (Dendroaspis polylepis polylepis) Explore P01416  Go to UniProtKB:  P01416

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	G [auth L], H [auth l]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.539	α = 90
b = 72.252	β = 91.99
c = 179.656	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Pletnev, S., Glanville, J., Kwong, P.D.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release