9KP5 | pdb_00009kp5

Crystal structure of Horse spleen L-ferritin mutant (E56F/R59F)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design of Aromatic Interaction Networks in a Protein Cage Modulated by Fluorescent Ligand Binding.

Hishikawa, Y.Suzuki, T.Maity, B.Noya, H.Yoshizawa, M.Asanuma, A.Katagiri, Y.Abe, S.Nagatoishi, S.Tsumoto, K.Ueno, T.

(2025) Adv Sci (Weinh) 12: e2417030-e2417030

  • DOI: https://doi.org/10.1002/advs.202417030
  • Primary Citation of Related Structures:  
    9KKP, 9KKR, 9KLE, 9KN7, 9KN8, 9KP2, 9KP5, 9KP7, 9KPA, 9KRS

  • PubMed Abstract: 

    Dynamic behavior of proteins, such as orientation changes of aromatic residues, plays an important role in controlling biomolecular functions. Protein design that can precisely control such dynamic behavior at the atomic level is a challenging issue. The study reports the development of a system capable of orientational changes of aromatic side chains upon ligand binding. Aromatic pockets are constructed on the inner surfaces of protein cages to bind polycyclic aromatic fluorescent molecules to the targeted position by π-π stacking interactions. X-ray crystal structural analysis indicated the cooperative orientation changes of the aromatic clusters around the pocket triggered by the ligand binding. A comparison of various ligands shows that the movement of aromatic clusters can be controlled depending on the ligand structures. Fluorescence quantum yield and fluorescence lifetime are enhanced due to isolation of the fluorescent molecules in an aromatic pocket. These findings provide an understanding of the unique molecular behavior and fluorescence properties of ligands due to the assembly of aromatic residues and a guideline for developing dynamically controlled supramolecular biomaterials.


  • Organizational Affiliation
    • School of Life Science and Technology, Institute of Science Tokyo, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan.

Macromolecules
Find similar proteins by:  (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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.928α = 90
b = 180.928β = 90
c = 180.928γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references