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- PDB-3glz: Human Transthyretin (TTR) complexed with(E)-3-(2-(trifluoromethyl... -

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Basic information

Entry
Database: PDB / ID: 3glz
TitleHuman Transthyretin (TTR) complexed with(E)-3-(2-(trifluoromethyl)benzylideneaminooxy)propanoic acid (inhibitor 11)
ComponentsTransthyretin
KeywordsHORMONE / TTR / AMYLOID / TRANSTHYRETIN / inhibitor / Amyloidosis / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Neuropathy / Polymorphism / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A
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/hydroxyisourate hydrolase domain / 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 ...Transthyretin/hydroxyisourate hydrolase domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-1BD / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsMohamedmohaideen, N.N. / Palaninathan, S.K. / Orlandini, E. / Sacchettini, J.C.
CitationJournal: Plos One / Year: 2009
Title: Novel transthyretin amyloid fibril formation inhibitors: synthesis, biological evaluation, and X-ray structural analysis
Authors: Palaninathan, S.K. / Mohamedmohaideen, N.N. / Orlandini, E. / Ortore, G. / Nencetti, S. / Lapucci, A. / Rossello, A. / Freundlich, J.S. / Sacchettini, J.C.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0774
Polymers27,5552
Non-polymers5222
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-9 kcal/mol
Surface area10550 Å2
MethodPISA
2
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1548
Polymers55,1094
Non-polymers1,0454
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6320 Å2
ΔGint-42 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.181, 84.939, 63.422
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-500-

1BD

21A-500-

1BD

31B-501-

1BD

41A-128-

HOH

51B-178-

HOH

61B-193-

HOH

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Components

#1: Protein Transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: UNP residues 21 to 147
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-1BD / 3-[({(1E)-[2-(trifluoromethyl)phenyl]methylidene}amino)oxy]propanoic acid / (E)-3-(2-(trifluoromethyl)benzylideneaminooxy)propanoic acid


Mass: 261.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10F3NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals of wt-TTR were obtained from 5-7 mg/mL protein solutions (in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, pH 7.0, 0.3 M ammonium sulfate) equilibrated against 2 M ammonium sulfate ...Details: Crystals of wt-TTR were obtained from 5-7 mg/mL protein solutions (in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, pH 7.0, 0.3 M ammonium sulfate) equilibrated against 2 M ammonium sulfate in hanging drops. TTR:ligand complexes were prepared from crystals soaked with a tenfold molar excess of ligand for more than two weeks., VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 5, 2007 / Details: mirrors
RadiationMonochromator: Varimax osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→63.37 Å / Num. all: 22460 / Num. obs: 22460 / % possible obs: 99.71 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.78→1.826 Å / % possible all: 99.94

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BMZ

1bmz


Resolution: 1.78→18.45 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.163 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27349 1149 5.1 %RANDOM
Rwork0.22417 ---
all0.22668 22460 --
obs0.22668 22460 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.604 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.62 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.78→18.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 36 158 1903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221788
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.962439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83923.52968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39615260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.177156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021336
X-RAY DIFFRACTIONr_nbd_refined0.210.2745
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21167
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.211
X-RAY DIFFRACTIONr_mcbond_it0.8771.51136
X-RAY DIFFRACTIONr_mcangle_it1.31321797
X-RAY DIFFRACTIONr_scbond_it2.423750
X-RAY DIFFRACTIONr_scangle_it3.2234.5642
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 88 -
Rwork0.287 1530 -
obs--99.94 %

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