7Z60 | pdb_00007z60

Human transthyretin (TTR) complexed with Quercetin 3-O-beta-D-galactoside

• PDB DOI: https://doi.org/10.2210/pdb7Z60/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2022-03-10 Released: 2022-05-18 
• Deposition Author(s): Ciccone, L., Braca, A., Orlandini, E., Nencetti, S.
• Funding Organization(s): Ministero dell Universita e della Ricerca

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Antioxidant Quercetin 3-O-Glycosylated Plant Flavonols Contribute to Transthyretin Stabilization

Ciccone, L., Tonali, N., Fruchart-Gaillard, C., Barlettani, L., Rossello, A., Braca, A., Orlandini, E., Nencetti, S.

(2022) Crystals (Basel) 12

• DOI: https://doi.org/10.3390/cryst12050638

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 28.15 kDa 
• Atom Count: 2,202 
• 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
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J6O (Subject of Investigation/LOI)	D [auth B]	2-[3,4-bis(oxidanyl)phenyl]-3-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5,7-bis(oxidanyl)chromen-4-one C21 H20 O12 OVSQVDMCBVZWGM-DTGCRPNFSA-N
IMD	E [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.23	α = 90
b = 85.6	β = 90
c = 64.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): Ciccone, L., Braca, A., Orlandini, E., Nencetti, S.

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Funding Organization	Location	Grant Number
Ministero dell Universita e della Ricerca	Italy	2017SNRXH3

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description