8XC9 | pdb_00008xc9

Amylase A in complex with acarbose

• PDB DOI: https://doi.org/10.2210/pdb8XC9/pdb

• Classification: HYDROLASE
• Organism(s): Alkalimonas delamerensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-08 Released: 2024-12-11 
• Deposition Author(s): Zhao, F., Xu, T.T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: in silico

Literature

Structure of amylase AmyA in complex with acarbose.

Zhao, F., Xu, T.T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 114.08 kDa 
• Atom Count: 8,054 
• Modeled Residue Count: 920 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmyA	A, B	498	Alkalimonas delamerensis	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for A0A1H4DB11 (Alkalimonas amylolytica) Explore A0A1H4DB11  Go to UniProtKB:  A0A1H4DB11

Oligosaccharides

Help

Entity ID: 2
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	C [auth E], D [auth F]	2	N/A	N/A
Glycosylation Resources
GlyTouCan:  G61060BJ GlyCosmos:  G61060BJ

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900110	C [auth E], D [auth F]	acarbose-derived trisaccharide	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140	α = 90
b = 140	β = 90
c = 84.18	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Zhao, F., Xu, T.T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release