8D9Z | pdb_00008d9z

Crystal structure of Cobra alpha-neurotoxin in complex with Centi-LNX-D09 antibody

• PDB DOI: https://doi.org/10.2210/pdb8D9Z/pdb

• Classification: IMMUNE SYSTEM,ANTITOXIN/TOXIN
• Organism(s): Homo sapiens, Naja nivea
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-06-12 Released: 2023-06-14 
• Deposition Author(s): Pletnev, S., Verardi, R., Tully, E.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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.198 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: in silico

Literature

Venom protection by antibody from a snakebite hyperimmune 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 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.1 kDa 
• Atom Count: 4,340 
• Modeled Residue Count: 508 
• Deposited Residue Count: 528 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centi-LNX-D09 Fab light chain	A	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Centi-LNX-D09 Fab heavy chain	B	237	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Long neurotoxin 1	C [auth D]	77	Naja nivea	Mutation(s): 0
UniProt
Find proteins for P01390 (Naja nivea) Explore P01390  Go to UniProtKB:  P01390

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	N [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.198 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.285	α = 90
b = 61.285	β = 90
c = 260.046	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Pletnev, S., Verardi, R., Tully, E.S., Glanville, J., Kwong, P.D.

---

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: 2023-06-14
  Type: Initial release
  
• Version 2.0: 2024-09-04
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-10-30
  Changes: Structure summary