4X0N

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6001 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pancreatic alpha-amylase
A
496Sus scrofaMutation(s): 0 
Gene Names: AMY2
EC: 3.2.1.1
Find proteins for P00690 (Sus scrofa)
Go to UniProtKB:  P00690
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Helianthamide
B
44Stichodactyla helianthusMutation(s): 0 
Find proteins for A0A0X1KGZ5 (Stichodactyla helianthus)
Go to UniProtKB:  A0A0X1KGZ5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6001 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.750α = 90.00
b = 103.280β = 90.00
c = 111.896γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanada--

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations