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

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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01426
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

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

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.