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- PDB-7eri: Crystal structure of V30M-TTR in complex with triclabendazole -

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Basic information

Entry
Database: PDB / ID: 7eri
TitleCrystal structure of V30M-TTR in complex with triclabendazole
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
Chem-JA9 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.813 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)35,4044
Polymers34,6852
Non-polymers7192
Water3,351186
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8098
Polymers69,3704
Non-polymers1,4394
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)42.993, 85.226, 63.727
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-201-

JA9

21A-201-

JA9

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17342.582 Da / Num. of mol.: 2 / Mutation: V50M
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-JA9 / 6-[2,3-bis(chloranyl)phenoxy]-5-chloranyl-2-methylsulfanyl-1H-benzimidazole / Triclabendazole


Mass: 359.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9Cl3N2OS / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 26.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, CaCl2, NaOAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→42.61 Å / Num. obs: 21609 / % possible obs: 98.6 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Rrim(I) all: 0.075 / Net I/σ(I): 19
Reflection shellResolution: 1.81→1.88 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2065 / CC1/2: 0.882 / Rpim(I) all: 0.219 / Rrim(I) all: 0.648 / % possible all: 95.4

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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: 1.813→35.641 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1080 5 %
Rwork0.189 --
obs0.1906 21596 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.813→35.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 42 186 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071869
X-RAY DIFFRACTIONf_angle_d0.9222552
X-RAY DIFFRACTIONf_dihedral_angle_d20.84652
X-RAY DIFFRACTIONf_chiral_restr0.086283
X-RAY DIFFRACTIONf_plane_restr0.006319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8132-1.89570.33151280.24682435X-RAY DIFFRACTION96
1.8957-1.99570.2881330.21062512X-RAY DIFFRACTION98
1.9957-2.12070.26171330.19962527X-RAY DIFFRACTION98
2.1207-2.28440.22261340.18152547X-RAY DIFFRACTION99
2.2844-2.51420.23031340.18332553X-RAY DIFFRACTION99
2.5142-2.87790.22331360.19212590X-RAY DIFFRACTION99
2.8779-3.62530.1931370.18412603X-RAY DIFFRACTION99
3.6253-35.6410.20671450.18132749X-RAY DIFFRACTION99

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