6GXV

Amylase in complex with acarbose

• PDB DOI: https://doi.org/10.2210/pdb6GXV/pdb

• Classification: HYDROLASE
• Organism(s): Alicyclobacillus sp.
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2018-06-27 Released: 2019-01-23 
• Deposition Author(s): Agirre, J., Moroz, O., Meier, S., Brask, J., Munch, A., Hoff, T., Andersen, C., Wilson, K.S., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.176 
• R-Value Work: 0.138 
• R-Value Observed: 0.140 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 112.28 kDa 
• Atom Count: 9,098 
• Modelled Residue Count: 962 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A-amylase	A, B	484	Alicyclobacillus sp.	Mutation(s): 0
UniProt
Find proteins for A0A3P8MUS3 (Alicyclobacillus sp) Explore A0A3P8MUS3  Go to UniProtKB:  A0A3P8MUS3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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)-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)-alpha-D-glucopyranose	E, F	4	N/A	N/A
Glycosylation Resources
GlyTouCan:  G53811MA GlyCosmos:  G53811MA

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	L [auth A], N [auth A], O [auth B], Q [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GLC	K [auth A], M [auth A], P [auth B], V [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
CA	G [auth A], I [auth A], J [auth A], R [auth B], T [auth B], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	H [auth A], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.176 
• R-Value Work: 0.138 
• R-Value Observed: 0.140 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.9	α = 90
b = 180.9	β = 90
c = 77.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
BUCCANEER	model building
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Agirre, J., Moroz, O., Meier, S., Brask, J., Munch, A., Hoff, T., Andersen, C., Wilson, K.S., Davies, G.J.

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.2: 2019-05-29
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2019-08-21
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary