4KY2 | pdb_00004ky2

Transthyretin in complex with the fluorescent folding sensor (E)-7-hydroxy-3-(4-hydroxy-3,5-dimethylstyryl)-4-methyl-2H-chromen-2-one

• PDB DOI: https://doi.org/10.2210/pdb4KY2/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-28 Released: 2013-08-28 
• Deposition Author(s): Connelly, S., Wilson, I.A., Choi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.174 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Bifunctional coumarin derivatives that inhibit transthyretin amyloidogenesis and serve as fluorescent transthyretin folding sensors.

Myung, N., Connelly, S., Kim, B., Park, S.J., Wilson, I.A., Kelly, J.W., Choi, S.

(2013) Chem Commun (Camb) 49: 9188-9190

• PubMed: 23989101 
• DOI: https://doi.org/10.1039/c3cc44667k
• Primary Citation Related Structures: 
  4KY2


• PubMed Abstract: 
  

  We describe coumarin derivatives that are non-fluorescent in aqueous buffers and that very selectively bind to transthyretin (TTR) in complex biological environments potently inhibiting TTR amyloidogenesis while also exhibiting sensitive off-on fluorescent sensing of the properly folded quaternary structure of TTR.

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Organizational Affiliation: 
• Department of New Drug Discovery and Development, Chungnam National University, Daejon, 305-764, Republic of Korea.
Department of Integrative Structural and Computational Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
College of Pharmacy, Gachon University, 534-2 Yeonsu 3-dong, Yeonsu-gu, Incheon 406-799, Republic of Korea.
Departments of Chemistry and Molecular and Experimental Medicine, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.2 kDa 
• Atom Count: 2,282 
• Modeled Residue Count: 231 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transthyretin	A, B	127	Homo sapiens	Mutation(s): 0  Gene Names: TTR, PALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens) Explore P02766  Go to UniProtKB:  P02766
PHAROS:  P02766 GTEx:  ENSG00000118271

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1W3	C [auth A], D [auth B]	7-hydroxy-3-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]-4-methyl-2H-chromen-2-one C20 H18 O4 YBZSRAYJXVITOB-GQCTYLIASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.174 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.793	α = 90
b = 85.646	β = 90
c = 63.562	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Connelly, S., Wilson, I.A., Choi, S.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description