5CZU

Crystal structure of FeCat-Fn

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Construction of an enterobactin analogue with symmetrically arranged monomer subunits of ferritin

Nakajima, H., Kondo, M., Nakane, T., Abe, S., Nakao, T., Watanabe, Y., Ueno, T.

(2015) Chem Commun (Camb) 51: 16609-16612

  • DOI: https://doi.org/10.1039/c5cc06904a
  • Primary Citation of Related Structures:  
    5AXS, 5CZU

  • PubMed Abstract: 

    A set of three catecholamide ligands mimicking the structure of enterobactin was constructed on ferritin, where the 3-fold symmetric arrangement of the monomer subunits served as a foundation to form a coordination space. Similar to enterobactin, the ligands showed strong affinity for the ferric ion and formed a tris-catechoyl complex. Crystallography revealed that the complex was embedded in the entrance of the 3-fold axis channel.

    • Organizational Affiliation: 

    Division of Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Osaka, 558-8585, Japan. [email protected].


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin light chain174Equus caballusMutation(s): 2 
Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus)
Explore P02791 
Go to UniProtKB:  P02791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02791
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4LF
Query on 4LF
Download Ideal Coordinates CCD File 
B [auth A]N-[2-[2,5-bis(oxidanylidene)pyrrol-1-yl]ethyl]-2,3-bis(oxidanyl)benzamide
C13 H12 N2 O5
BABSFPLAEBUXOA-UHFFFAOYSA-N
CD
Query on CD
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]		CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL
Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE
Query on FE
Download Ideal Coordinates CCD File 
H [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.07α = 90
b = 181.07β = 90
c = 181.07γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary