1MXD

Structure of a (Ca,Zn)-dependent alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei

• PDB DOI: https://doi.org/10.2210/pdb1MXD/pdb

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


• Deposited: 2002-10-02 Released: 2003-06-10 
• Deposition Author(s): Linden, A., Mayans, O., Meyer-Klaucke, W., Antranikian, G., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.48 kDa 
• Atom Count: 4,007 
• Modelled Residue Count: 435 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha amylase	A	435	Pyrococcus woesei	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for Q7LYT7 (Pyrococcus woesei) Explore Q7LYT7  Go to UniProtKB:  Q7LYT7

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-(1-4)-alpha-D-glucopyranose	B, C, D, E	3	N/A	N/A
Glycosylation Resources
GlyTouCan:  G66431MI GlyCosmos:  G66431MI

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	M [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
ZN	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	N [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	L [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900007	B, C, D, E	alpha-acarbose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.837	α = 90
b = 77.207	β = 90
c = 106.569	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-10 
Deposition Author(s): Linden, A., Mayans, O., Meyer-Klaucke, W., Antranikian, G., Wilmanns, M.

Revision History  

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary