8S72 | pdb_00008s72

Crystal structure of neutralizing Fab Eq4.Dp46-3D from equine antivenom bound to a consensus short chain three finger alpha-neurotoxin.

PDB DOI: https://doi.org/10.2210/pdb8S72/pdb

Classification: ANTITOXIN
Organism(s): synthetic construct, Equus caballus
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2024-02-28 Released: 2025-09-10
Deposition Author(s): Ayres, F., Wibmer, C.K.
Funding Organization(s): Wellcome Trust, Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free:
0.249 (Depositor), 0.252 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

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

Ayres, F., Patel, R., Casewell, N., Wibmer, C.K.

To be published.

Macromolecule Content

Total Structure Weight: 108.99 kDa
Atom Count: 7,512
Modeled Residue Count: 1,001
Deposited Residue Count: 1,028
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short neurotoxin 1	A [auth N], B [auth A]	64	synthetic construct	Mutation(s): 7
UniProt
Find proteins for P01426 (Naja pallida) Explore P01426 Go to UniProtKB: P01426
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01426
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.	C [auth X], E [auth H]	233	Equus caballus	Mutation(s): 0 Gene Names: IgHV4

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab domain from antivenom neutralizing antibody Eq4.Dp46-3D.	D [auth Y], F [auth L]	217	Equus caballus	Mutation(s): 0 Gene Names: IgLV

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	C [auth X], E [auth H]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.249 (Depositor), 0.252 (DCC)
R-Value Work: 0.228 (Depositor), 0.230 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 294.846	α = 90
b = 294.846	β = 90
c = 99.525	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	227858/Z/23/Z
Royal Society	United Kingdom	201782

Revision History (Full details and data files)

Version 1.0: 2025-09-10
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.