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- PDB-6ti9: Human transthyretin (TTR) complexed with (E)-3-(((3,5-dibromo-2-h... -

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Basic information

Entry
Database: PDB / ID: 6ti9
TitleHuman transthyretin (TTR) complexed with (E)-3-(((3,5-dibromo-2-hydroxybenzylidene)amino)oxy)propanoic acid.
ComponentsTransthyretin
KeywordsPROTEIN TRANSPORT / Transthyretin / TTR / inhibitor / complex
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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-ND5 / S-1,2-PROPANEDIOL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsCiccone, L. / Nencetti, S. / Orlandini, E. / Rossello, A. / Legrand, P. / Shepard, W.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Monoaryl derivatives as transthyretin fibril formation inhibitors: Design, synthesis, biological evaluation and structural analysis.
Authors: Ciccone, L. / Nencetti, S. / Tonali, N. / Fruchart-Gaillard, C. / Shepard, W. / Nuti, E. / Camodeca, C. / Rossello, A. / Orlandini, E.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,6477
Polymers27,6692
Non-polymers9785
Water3,297183
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29414
Polymers55,3384
Non-polymers1,95710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8170 Å2
ΔGint-36 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.130, 85.810, 63.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

ND5

21A-201-

ND5

31B-502-

ND5

41B-502-

ND5

51B-502-

ND5

61B-502-

ND5

71A-328-

HOH

81B-620-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13834.413 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-ND5 / 3-[(~{E})-[3,5-bis(bromanyl)-2-oxidanyl-phenyl]methylideneamino]oxypropanoic acid


Mass: 366.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9Br2NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 4.93 mg/mL, Tris pH 8.0, 150mM NaCl. Precipitant: 24% PEG 600, 0.2M imidazole malate pH 5.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.919491 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919491 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 42796 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 1 / Net I/σ(I): 1.96
Reflection shellResolution: 1.45→1.46 Å / Num. unique obs: 60556 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+23 / Resolution: 1.45→24.584 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.41 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1824 2138 5 %
Rwork0.1547 40630 -
obs0.1561 42768 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.94 Å2 / Biso mean: 27.1146 Å2 / Biso min: 13.39 Å2
Refinement stepCycle: final / Resolution: 1.45→24.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 90 183 2051
Biso mean--53.24 38.33 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.45-1.48370.31111410.26022677
1.4837-1.52080.27771390.21392644
1.5208-1.5620.24551410.18432667
1.562-1.60790.22041400.15992669
1.6079-1.65980.19581410.14762677
1.6598-1.71910.22331420.14262696
1.7191-1.78790.17241420.13892689
1.7879-1.86930.17421400.13542666
1.8693-1.96780.16821420.1262690
1.9678-2.0910.15781420.12532712
2.091-2.25240.16751430.12942709
2.2524-2.47880.18391430.13952712
2.4788-2.83710.19371440.15362742
2.8371-3.57260.18711470.15692787

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