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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.220 (Depositor), 0.246 (DCC)
R-Value Work:
0.182 (Depositor)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02766
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J6O (Subject of Investigation/LOI) Query on J6O Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	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		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.220 (Depositor), 0.246 (DCC)
R-Value Work: 0.182 (Depositor)
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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-18

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-05-18
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2025-10-01
Changes: Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.