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- PDB-4tq8: Dual binding mode for 3-(9H-fluoren-9-ylideneaminooxy)propanoic a... -

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Basic information

Entry
Database: PDB / ID: 4tq8
TitleDual binding mode for 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid binding to Human transthyretin (TTR)
ComponentsTransthyretin
KeywordsHORMONE / TTR / inhibitor 15 / forward and reverse binding modes / amyloid inhibitor / Polyethylene glycol crystallization
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/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
3-[(9H-fluoren-9-ylideneamino)oxy]propanoic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 Å
AuthorsCiccone, L. / Orlandini, E. / Nencetti, S. / Rossello, A. / Stura, E.A.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2015
Title: X-ray crystal structure and activity of fluorenyl-based compounds as transthyretin fibrillogenesis inhibitors.
Authors: Ciccone, L. / Nencetti, S. / Rossello, A. / Tepshi, L. / Stura, E.A. / Orlandini, E.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,2136
Polymers27,5552
Non-polymers6594
Water4,179232
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,42712
Polymers55,1094
Non-polymers1,3178
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)43.140, 86.040, 63.480
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-

7BD

21B-201-

7BD

31A-303-

HOH

41B-321-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P02766
#2: Chemical ChemComp-7BD / 3-[(9H-fluoren-9-ylideneamino)oxy]propanoic acid / 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid


Mass: 267.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: Protein: 5 mg/ml 1 milli-M ligand Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) 40% (24% MPEG-5K, 0.1 M sodium acetate, pH 5.5) Drops: 1 micro-L protein-ligand complex 1 ...Details: Protein: 5 mg/ml 1 milli-M ligand Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) 40% (24% MPEG-5K, 0.1 M sodium acetate, pH 5.5) Drops: 1 micro-L protein-ligand complex 1 micro-L precipitant. Cryoprotectant:: 40% (12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 12.5 % DMSO + 12.5 % 1,4-dioxane), 25% MPEG 5K, 0.1 M sodium propionate, sodium cacodylate, Bis-Tris-propane(65% component A pH 4; 35% B pH 9.5 and 1 milli-M ligand.
PH range: 5.5-6.0 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 26, 2014
RadiationMonochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.52→43.1 Å / Num. all: 37141 / Num. obs: 37078 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.73 % / Rmerge(I) obs: 0.145 / Rsym value: 0.137 / Net I/σ(I): 11.9
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.01 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Cootmodel building
XDSdata scaling
MOLREPphasing
MxCuBEdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.52→38.56 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.748 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 1854 5 %RANDOM
Rwork0.18605 ---
obs0.18728 35223 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0 Å2
2---0.54 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.52→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 48 232 2074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192173
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.9912990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19224.19493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87915336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4511510
X-RAY DIFFRACTIONr_chiral_restr0.150.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211744
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.521→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 135 -
Rwork0.379 2561 -
obs--98.61 %

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