9HH0 | pdb_00009hh0

Crystal structure of recombinant soman-aged swine butyrylcholinesterase

PDB DOI: https://doi.org/10.2210/pdb9HH0/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2024-11-20 Released: 2025-12-03
Deposition Author(s): Brazzolotto, X., Nachon, F.
Funding Organization(s): French Ministry of Armed Forces

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free:
0.236 (Depositor), 0.212 (DCC)
R-Value Work:
0.195 (Depositor)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

An improved nerve agent bioscavenger based on the fast self-reactivation mechanism of porcine butyrylcholinesterase.

Brazzolotto, X., Lushchekina, S., Nachon, F.

(2026) Protein Sci 35: e70467-e70467

PubMed: 41556466 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70467
Primary Citation Related Structures:
9HGZ, 9HH0

PubMed Abstract:
Inhibition of cholinesterases by warfare nerve agents is characterized by forming a stable covalent adduct on the active site serine. We report the fast, spontaneous hydrolysis of the adduct formed by chiral phosphonate nerve agents and porcine butyrylcholinesterase. Fast hydrolysis only occurs with the most toxic enantiomer. Crystal structures of apo and soman-inhibited porcine butyrylcholinesterase highlight the potential role of the Acyl-Binding-loop in the rate of spontaneous reactivation, further supported by molecular dynamics. Introducing mutations in human butyrylcholinesterase to mimic the loop of the porcine enzyme converted it into a fast, self-regenerating bioscavenger, particularly for V-agents. Characterization of the reactivation mechanism by molecular dynamics and quantum mechanics simulations supports that the quicker hydrolysis of the nerve agent adducts originates from its better hydration. This work represents a breakthrough in the design of butyrylcholinesterase-based bioscavengers of nerve agents.

Organizational Affiliation

Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, Brétigny sur Orge, France.

Macromolecule Content

Total Structure Weight: 246.88 kDa
Atom Count: 17,379
Modeled Residue Count: 2,074
Deposited Residue Count: 2,116
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylic ester hydrolase	A, B, C, D	529	Sus scrofa	Mutation(s): 0 Gene Names: BCHE EC: 3.1.1
UniProt
Find proteins for A0A4X1VEU5 (Sus scrofa) Explore A0A4X1VEU5 Go to UniProtKB: A0A4X1VEU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1VEU5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	2		N-Glycosylation	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I, L	2		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain L Interactions & Density Focus chain H Focus chain I Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	4		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K	3		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], O [auth A], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain DA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain DA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain DA [auth B]	DA [auth B] KA [auth C] LA [auth C] U [auth A] V [auth A] DA [auth B], KA [auth C], LA [auth C], U [auth A], V [auth A], W [auth A], X [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain DA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]
GB (Subject of Investigation/LOI) Query on GB Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain MA [auth D] SDF format, chain HA [auth C] SDF format, chain BA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain BA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain BA [auth B]	BA [auth B], HA [auth C], MA [auth D], S [auth A]	METHYLPHOSPHONIC ACID ESTER GROUP C H₅ O₃ P YACKEPLHDIMKIO-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain S [auth A] Interactions & Density Focus chain BA [auth B] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain S [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain CA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain CA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain CA [auth B]	CA [auth B] IA [auth C] JA [auth C] P [auth A] Q [auth A] CA [auth B], IA [auth C], JA [auth C], P [auth A], Q [auth A], R [auth A], T [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth A] Interactions & Density Focus chain CA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain NA [auth D] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B]	EA [auth B], FA [auth B], GA [auth B], NA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain NA [auth D] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain NA [auth D]