3AYQ | pdb_00003ayq

Crystal structure of inhibitor bound lysozyme from Meretrix lusoria

• PDB DOI: https://doi.org/10.2210/pdb3AYQ/pdb

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


• Deposited: 2011-05-13 Released: 2012-05-23 
• Deposition Author(s): Yoneda, K., Kuwano, Y., Usui, T., Ogata, M., Suzuki, A., Araki, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.231 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.245 (DCC) 

Starting Model: experimental

Literature

Crystal structure of inhibitor bound lysozyme from Meretrix lusoria

Yoneda, K., Kuwano, Y., Usui, T., Ogata, M., Suzuki, A., Araki, T.

To be published.

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: 14.2 kDa 
• Atom Count: 1,129 
• Modeled 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	D 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-(1-4)-N-[(5S,6R)-5-hydroxy-6-(hydroxymethyl)-2-oxo-5,6-dihydro-2H-pyran-3-yl]acetamide	B	4		N/A
Glycosylation Resources
GlyTouCan: G09106QR GlyCosmos: G09106QR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.231 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.245 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.123	α = 90
b = 42.123	β = 90
c = 122.856	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: 2012-05-23 
Deposition Author(s): Yoneda, K., Kuwano, Y., Usui, T., Ogata, M., Suzuki, A., Araki, T.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• 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
• Version 2.2: 2024-10-09
  Changes: Structure summary