4FJR | pdb_00004fjr

Mode of interaction of Merocyanine 540 with HEW Lysozyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.246 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0UFClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


Literature

Mode of interaction of Merocyanine 540 dye with lysozyme

Mitra, P., Banerjee, M., Basu, S., Biswas, S.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0UF
Query on 0UF
Download Ideal Coordinates CCD File 
D [auth A]3-[(2E)-2-[(2Z)-4-(1,3-dibutyl-4,6-dioxo-2-thioxotetrahydropyrimidin-5(2H)-ylidene)but-2-en-1-ylidene]-1,3-benzoxazol-3(2H)-yl]propane-1-sulfonic acid
C26 H33 N3 O6 S2
SKDUSRXOWAXOCO-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.77α = 90
b = 78.77β = 90
c = 37.02γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
CNSrefinement
AUTOMARdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0UFClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary