5E0F

Human pancreatic alpha-amylase in complex with mini-montbretin A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history. 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6OBX 6OCN


Literature

Human pancreatic alpha-amylase in complex with mini-montbretin A

Caner, S., Brayer, G.D.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pancreatic alpha-amylase496Homo sapiensMutation(s): 0 
Gene Names: AMY2A
EC: 3.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04746 (Homo sapiens)
Explore P04746 
Go to UniProtKB:  P04746
PHAROS:  P04746
GTEx:  ENSG00000243480 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04746
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5J7
Query on 5J7
Download Ideal Coordinates CCD File 
B [auth A]5,7-dihydroxy-4-oxo-2-(3,4,5-trihydroxyphenyl)-4H-chromen-3-yl 6-deoxy-2-O-{6-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-beta-D-glucopyranosyl}-alpha-L-mannopyranoside
C36 H36 O20
YHIHWLPOKDIYGF-ZLGVOOGTSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Binding Affinity Annotations 
IDSourceBinding Affinity
5J7 BindingDB:  5E0F Ki: 93.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.32α = 90
b = 73.19β = 90
c = 133.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaCIHR MOP-111082

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 2.0: 2020-01-08
    Changes: Author supporting evidence, Derived calculations, Polymer sequence
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-10-30
    Changes: Structure summary