1B2Y | pdb_00001b2y

STRUCTURE OF HUMAN PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH THE CARBOHYDRATE INHIBITOR ACARBOSE

• PDB DOI: https://doi.org/10.2210/pdb1B2Y/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1998-12-03 Released: 2000-02-16 
• Deposition Author(s): Nahoum, V., Payan, F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.217 (Depositor) 
• R-Value Work: 
  0.191 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of human pancreatic alpha-amylase in complex with carbohydrate and proteinaceous inhibitors.

Nahoum, V., Roux, G., Anton, V., Rouge, P., Puigserver, A., Bischoff, H., Henrissat, B., Payan, F.

(2000) Biochem J 346 Pt 1: 201-208

• PubMed: 10657258 
• Primary Citation Related Structures: 
  1B2Y


• PubMed Abstract: 
  

  Crystal structures of human pancreatic alpha-amylase (HPA) in complex with naturally occurring inhibitors have been solved. The tetrasaccharide acarbose and a pseudo-pentasaccharide of the trestatin family produced identical continuous electron densities corresponding to a pentasaccharide species, spanning the -3 to +2 subsites of the enzyme, presumably resulting from transglycosylation. Binding of the acarviosine core linked to a glucose residue at subsites -1 to +2 appears to be a critical part of the interaction process between alpha-amylases and trestatin-derived inhibitors. Two crystal forms, obtained at different values of pH, for the complex of HPA with the protein inhibitor from Phaseolus vulgaris (alpha-amylase inhibitor) have been solved. The flexible loop typical of the mammalian alpha-amylases was shown to exist in two different conformations, suggesting that loop closure is pH-sensitive. Structural information is provided for the important inhibitor residue, Arg-74, which has not been observed previously in structural analyses.

---

Organizational Affiliation: 
• Architecture et Fonction des Macromolécules Biologiques, CNRS-IFR1, 31 Chemin Joseph Aiguier, 13402 Marseille, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.8 kDa 
• Atom Count: 4,107 
• 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  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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	4	N/A	N/A
Glycosylation Resources
GlyTouCan: G42476FD GlyCosmos: G42476FD

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.217 (Depositor) 
• R-Value Work:  0.191 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.11	α = 90
b = 75.1	β = 90
c = 137.13	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-16 
Deposition Author(s): Nahoum, V., Payan, F.

Revision History  

• Version 1.0: 2000-02-16
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2017-10-25
  Changes: Atomic model, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 4.0: 2023-02-22
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 4.1: 2023-09-20
  Changes: Data collection, Refinement description
• Version 4.2: 2024-11-06
  Changes: Structure summary