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- PDB-7erh: Crystal structure of WT-TTR in complex with bithionol -

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Basic information

Entry
Database: PDB / ID: 7erh
TitleCrystal structure of WT-TTR in complex with bithionol
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidosis / Inhibitor / Complex
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family
Similarity search - Domain/homology
2,2'-sulfanediylbis(4,6-dichlorophenol) / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYokoyama, T. / Kashihara, M. / Mizuguchi, M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Repositioning of the Anthelmintic Drugs Bithionol and Triclabendazole as Transthyretin Amyloidogenesis Inhibitors.
Authors: Yokoyama, T. / Kashihara, M. / Mizuguchi, M.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0575
Polymers34,6212
Non-polymers4363
Water3,315184
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,11410
Polymers69,2424
Non-polymers8726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6940 Å2
ΔGint-73 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.342, 85.371, 64.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21B-310-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17310.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-B1T / 2,2'-sulfanediylbis(4,6-dichlorophenol)


Mass: 356.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H6Cl4O2S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 26.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, CaCl2, Tris-HCl pH 8, bithionol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→37.93 Å / Num. obs: 34392 / % possible obs: 99.1 % / Redundancy: 9.2 % / CC1/2: 0.997 / Rpim(I) all: 0.032 / Rrim(I) all: 0.096 / Net I/σ(I): 14.9
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3327 / CC1/2: 0.799 / Rpim(I) all: 0.356 / Rrim(I) all: 1.111 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PWE

4pwe


Resolution: 1.55→30.083 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1719 5 %
Rwork0.1935 --
obs0.1947 34380 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→30.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 21 184 1978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051866
X-RAY DIFFRACTIONf_angle_d0.7542552
X-RAY DIFFRACTIONf_dihedral_angle_d18.87659
X-RAY DIFFRACTIONf_chiral_restr0.083289
X-RAY DIFFRACTIONf_plane_restr0.006322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59460.24971390.23552638X-RAY DIFFRACTION98
1.5946-1.64610.26621410.2192681X-RAY DIFFRACTION99
1.6461-1.70490.27281410.2172668X-RAY DIFFRACTION99
1.7049-1.77310.23541410.21882687X-RAY DIFFRACTION99
1.7731-1.85380.23011420.2062688X-RAY DIFFRACTION99
1.8538-1.95150.21621420.19142714X-RAY DIFFRACTION99
1.9515-2.07380.22971420.18922694X-RAY DIFFRACTION99
2.0738-2.23390.21031430.18222719X-RAY DIFFRACTION100
2.2339-2.45860.24491440.18652726X-RAY DIFFRACTION100
2.4586-2.81410.23591460.19822770X-RAY DIFFRACTION100
2.8141-3.54460.20241460.19692785X-RAY DIFFRACTION100
3.5446-30.0830.19641520.18392891X-RAY DIFFRACTION99

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