1RP9

Crystal structure of barley alpha-amylase isozyme 1 (amy1) inactive mutant d180a in complex with acarbose

• PDB DOI: https://doi.org/10.2210/pdb1RP9/pdb

• Classification: HYDROLASE
• Organism(s): Hordeum vulgare
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2003-12-03 Released: 2005-06-07 
• Deposition Author(s): Robert, X., Haser, R., Aghajari, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.63 kDa 
• Atom Count: 3,663 
• Modelled Residue Count: 404 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase type 1 isozyme	A	405	Hordeum vulgare	Mutation(s): 1  Gene Names: AMY1.1 EC: 3.2.1.1
UniProt
Find proteins for P00693 (Hordeum vulgare) Explore P00693  Go to UniProtKB:  P00693

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	3	N/A	N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	3	N/A	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.73	α = 90
b = 73.54	β = 90
c = 61.06	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-07 
Deposition Author(s): Robert, X., Haser, R., Aghajari, N.

Revision History  

• Version 1.0: 2005-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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, Derived calculations, Structure summary
• Version 2.1: 2021-10-27
  Changes: Database references, Structure summary
• Version 2.2: 2023-08-23
  Changes: Data collection, Refinement description