3AB6

Crystal structure of NAG3 bound lysozyme from Meretrix lusoria

• PDB DOI: https://doi.org/10.2210/pdb3AB6/pdb

• Classification: HYDROLASE
• Organism(s): Meretrix lusoria
• Mutation(s): No 


• Deposited: 2009-12-01 Released: 2010-12-01 
• Deposition Author(s): Yoneda, K., Kuwano, Y., Araki, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.225 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 14.01 kDa 
• Atom Count: 1,153 
• Modelled Residue Count: 122 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A	122	Meretrix lusoria	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P86383 (Meretrix lusoria) Explore P86383  Go to UniProtKB:  P86383

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	B	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.225 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.61	α = 90
b = 41.61	β = 90
c = 123.208	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Yoneda, K., Kuwano, Y., Araki, T.

Revision History  

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-11-20
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary