4X0N | pdb_00004x0n

Porcine pancreatic alpha-amylase in complex with helianthamide, a novel proteinaceous inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4X0N/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Sus scrofa, Stichodactyla helianthus
• Mutation(s): No 


• Deposited: 2014-11-21 Released: 2015-11-25 
• Deposition Author(s): Williams, L.K., Brayer, G.D.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.226 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structural Templating and Guided Refolding of the Potent Naturally Occurring Peptide Helianthamide Within the Active Site of Amylase, a Diabetes and Obesity Therapeutic Target

Tysoe, C., Williams, L.K., Keyzers, R., Nguyen, N.T., Aguda, A., Zhang, X., Tarling, C.A., Andersen, R.J., Brayer, G.D., Withers, S.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 60.24 kDa 
• Atom Count: 4,453 
• Modeled Residue Count: 540 
• Deposited Residue Count: 540 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pancreatic alpha-amylase	A	496	Sus scrofa	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for P00690 (Sus scrofa) Explore P00690  Go to UniProtKB:  P00690

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Helianthamide	B	44	Stichodactyla helianthus	Mutation(s): 0
UniProt
Find proteins for A0A0X1KGZ5 (Stichodactyla helianthus) Explore A0A0X1KGZ5  Go to UniProtKB:  A0A0X1KGZ5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.226 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.75	α = 90
b = 103.28	β = 90
c = 111.896	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Williams, L.K., Brayer, G.D.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 2.0: 2020-01-08
  Changes: Author supporting evidence, Polymer sequence
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-10-09
  Changes: Structure summary