Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.44 kDa 
• Atom Count: 5825 
• Modelled Residue Count: 691 
• Deposited Residue Count: 719 
• Unique protein chains: 2

1DHK

STRUCTURE OF PORCINE PANCREATIC ALPHA-AMYLASE

• DOI: 10.2210/pdb1DHK/pdb

• Classification: COMPLEX (HYDROLASE/INHIBITOR)
• Organism(s): Sus scrofa, Phaseolus vulgaris
• Mutation(s): No 


• Deposited: 1996-10-14 Released: 1997-12-24 
• Deposition Author(s): Bompard-Gilles, C., Payan, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.220 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 

Literature

Substrate mimicry in the active center of a mammalian alpha-amylase: structural analysis of an enzyme-inhibitor complex.

Bompard-Gilles, C., Rousseau, P., Rouge, P., Payan, F.

(1996) Structure 4: 1441-1452

• PubMed: 8994970 
• DOI: 10.1016/s0969-2126(96)00151-7
• Primary Citation of Related Structures:  
  1DHK


• PubMed Abstract: 
  

alpha-Amylases catalyze the hydrolysis of glycosidic linkages in starch and other related polysaccharides. The alpha-amylase inhibitor (alpha-Al) from the bean Phaseolus vulgaris belongs to a family of plant defence proteins and is a potent inhibitor of mammalian alpha-amylases. The structure of pig pancreatic alpha-amylase (PPA) in complex with both a carbohydrate inhibitor (acarbose) and a proteinaceous inhibitor (Tendamistat) is known, but the catalytic mechanism is poorly understood.

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Related Citations: 

• Crystallization and Preliminary X-Ray Analysis of Pig Pancreatic Alpha-Amylase in Complex with a Bean Lectin-Like Inhibitor
  Gilles, C., Rousseau, P., Rouge, P., Payan, F.
  (1996) Acta Crystallogr D Biol Crystallogr 52: 581

• The Active Center of a Mammalian Alpha-Amylase. Structure of the Complex of a Pancreatic Alpha-Amylase with a Carbohydrate Inhibitor Refined to 2.2-A Resolution
  Qian, M., Haser, R., Buisson, G., Duee, E., Payan, F.
  (1994) Biochemistry 33: 6284

• Structure and Molecular Model Refinement of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
  Qian, M., Haser, R., Payan, F.
  (1993) J Mol Biol 231: 785

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Organizational Affiliation: 

AFMB-IBSM-CNRS, Marseille, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PORCINE PANCREATIC ALPHA-AMYLASE	A	496	Sus scrofa	Mutation(s): 0  Gene Names: AMY2 EC: 3.2.1.1
Find proteins for P00690 (Sus scrofa) Explore P00690  Go to UniProtKB:  P00690

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BEAN LECTIN-LIKE INHIBITOR	B	223	Phaseolus vulgaris	Mutation(s): 0  Gene Names: LLP, Alpha-AI1
Find proteins for P02873 (Phaseolus vulgaris) Explore P02873  Go to UniProtKB:  P02873

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	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: 1.85 Å
• R-Value Free: 0.220 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.6	α = 90
b = 79.4	β = 91.54
c = 68	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-10-14 
• Released Date: 1997-12-24 
Deposition Author(s): Bompard-Gilles, C., Payan, F.

Revision History  

• Version 1.0: 1997-12-24
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2019-12-25
  Changes: Data collection, Database references, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary