9XE5 | pdb_00009xe5

Defensin-like inhibitor of mammalian amylases, magnificamide-2, from the sea anemone Heteractis magnifica

• PDB DOI: https://doi.org/10.2210/pdb9XE5/pdb

• Classification: TOXIN
• Organism(s): Heteractis magnifica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-27 Released: 2026-10-28 
• Deposition Author(s): Menshov, A., Paramonov, A., Popkova, D., Shenkarev, Z., Leychenko, E.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Novel beta-defensin-like marine miniprotein magnificamide-2 with a remarkable potency in inhibiting mammalian alpha-amylases.

Popkova, D., Menshov, A., Sintsova, O., Paramonov, A., Kalina, R., Panina, I., Kalinovskii, A., Osmakov, D., Shamatova, M., Dmitrenok, P., Chugunov, A., Kozlov, S., Efremov, R., Shenkarev, Z., Gladkikh, I., Leychenko, E.

(2026) Int J Biol Macromol 376: 153418-153418

• PubMed: 42419540 
• DOI: https://doi.org/10.1016/j.ijbiomac.2026.153418
• Primary Citation Related Structures: 
  9XE5


• PubMed Abstract: 
  

  Reducing polysaccharide degradation through inhibition of α-amylases and α-glucosidases is one of the strategies for glycemic control in the treatment of diabetes mellitus. Here we report the identification and characterization of a new β-defensin-like miniprotein magnificamide-2 (Mgf-2), one of the most potent inhibitors of mammalian α-amylases with subnanomolar binding affinity (K _i of recombinant Mgf-2 is 0.029 nM against human pancreatic α-amylase, 0.057 nM against human salivary α-amylase, and 0.011 nM against porcine pancreatic α-amylase). Using nuclear magnetic resonance (NMR) spectroscopy, ensemble protein-protein docking, and molecular dynamics (MD) simulations, the key structural determinants responsible for this ultra-tight inhibition were identified, which was subsequently confirmed by site-directed mutagenesis experiments. The β1-β2 loop containing the inhibitory motif ⁷ YIYH ¹⁰ plays a crucial role in the inhibitor-enzyme interaction by forming an extensive hydrophobic interface with the hydrophobic "rim" around the α-amylase active site. The data obtained enhance our understanding of the molecular mechanisms underlying high-affinity α-amylase inhibition and provide valuable insights into the design of novel proteinaceous α-amylase inhibitors for the treatment and prevention of postprandial hyperglycemia.

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Organizational Affiliation: 
• G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia. Electronic address: [e-mail].
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Scientific Research Institute for Systems Biology and Medicine, Moscow, Russia.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Scientific Research Institute for Systems Biology and Medicine, Moscow, Russia; National Research University Higher School of Economics, Moscow, Russia.
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 4.79 kDa 
• Atom Count: 328 
• Modeled Residue Count: 44 
• Deposited Residue Count: 44 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase inhibitor magnificamide	A	44	Heteractis magnifica	Mutation(s): 0
UniProt
Find proteins for C0HK71 (Heteractis magnifica) Explore C0HK71  Go to UniProtKB:  C0HK71

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Menshov, A., Paramonov, A., Popkova, D., Shenkarev, Z., Leychenko, E.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	21-74-20147

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release