1UA3 | pdb_00001ua3

Crystal structure of the pig pancreatic a-amylase complexed with malto-oligosaccharides

• PDB DOI: https://doi.org/10.2210/pdb1UA3/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2003-02-27 Released: 2003-10-14 
• Deposition Author(s): Payan, F., Qian, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.196 (Depositor) 
• R-Value Work: 
  0.175 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Crystal Structure of the Pig Pancreatic alpha-Amylase Complexed with Malto-Oligosaccharides

Payan, F., Qian, M.

(2003) J Protein Chem 22: 275-284

• PubMed: 12962327 
• DOI: https://doi.org/10.1023/a:1025072520607
• Primary Citation Related Structures: 
  1UA3


• PubMed Abstract: 
  

  The structural X-ray map of a pig pancreatic alpha-amylase crystal soaked (and flash-frozen) with a maltopentaose substrate showed a pattern of electron density corresponding to the binding of oligosaccharides at the active site and at three surface binding sites. The electron density region observed at the active site, filling subsites-3 through-1, was interpreted in terms of the process of enzyme-catalyzed hydrolysis undergone by maltopentaose. Because the expected conformational changes in the "flexible loop" that constitutes the surface edge of the active site were not observed, the movement of the loop may depend on aglycone site being filled. The crystal structure was refined at 2.01 A resolution to an R factor of 17.0% ( R(free) factor of 19.8%). The final model consists of 3910 protein atoms, one calcium ion, two chloride ions, 103 oligosaccharide atoms, 761 atoms of water molecules, and 23 ethylene glycol atoms.

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Organizational Affiliation: 
• Architecture et Fonction des Macromolécules Biologiques, CNRS and Universities Aix-Marseille I and II, Marseille, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.5 kDa 
• Atom Count: 4,827 
• Modeled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase, pancreatic	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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan: G96370VA GlyCosmos: G96370VA GlyGen: G96370VA

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	H [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
EDO	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009	C, D	alpha-maltotriose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.196 (Depositor) 
• R-Value Work:  0.175 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.781	α = 90
b = 113.183	β = 90
c = 116.924	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-14 
Deposition Author(s): Payan, F., Qian, M.

Revision History  

• Version 1.0: 2003-10-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary