5E0F | pdb_00005e0f

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

• PDB DOI: https://doi.org/10.2210/pdb5E0F/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2015-09-28 Released: 2016-09-07 
• Deposition Author(s): Caner, S., Brayer, G.D.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 56.8 kDa 
• Atom Count: 4,480 
• Modeled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pancreatic alpha-amylase	A	496	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5J7	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	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [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

Binding Affinity Annotations
ID	Source	Binding 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 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.32	α = 90
b = 73.19	β = 90
c = 133.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Caner, S., Brayer, G.D.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	CIHR MOP-111082

Revision History  

• 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