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- PDB-6eoy: Transthyretin in complex with 4-(1,3-Benzothiazol-2-yl)-2-methyla... -

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Basic information

Entry
Database: PDB / ID: 6eoy
TitleTransthyretin in complex with 4-(1,3-Benzothiazol-2-yl)-2-methylaniline
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin / amyloid / TTR amyloid inhibitor
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / 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
4-(1,3-benzothiazol-2-yl)-2-methyl-aniline / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsLeite, J.P. / Gales, L.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Targeting transthyretin in Alzheimer's disease: Drug discovery of small-molecule chaperones as disease-modifying drug candidates for Alzheimer's disease.
Authors: Cotrina, E.Y. / Santos, L.M. / Rivas, J. / Blasi, D. / Leite, J.P. / Liz, M.A. / Busquets, M.A. / Planas, A. / Prohens, R. / Gimeno, A. / Jimenez-Barbero, J. / Gales, L. / Llop, J. / ...Authors: Cotrina, E.Y. / Santos, L.M. / Rivas, J. / Blasi, D. / Leite, J.P. / Liz, M.A. / Busquets, M.A. / Planas, A. / Prohens, R. / Gimeno, A. / Jimenez-Barbero, J. / Gales, L. / Llop, J. / Quintana, J. / Cardoso, I. / Arsequell, G.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)25,6934
Polymers25,2122
Non-polymers4812
Water1,910106
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3868
Polymers50,4244
Non-polymers9614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Unit cell
Length a, b, c (Å)42.863, 85.509, 64.275
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-

BM8

21A-201-

BM8

31A-201-

BM8

41A-201-

BM8

51A-201-

BM8

61B-201-

BM8

71B-201-

BM8

81B-201-

BM8

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 22 or resid 24...
21(chain B and (resid 10 through 22 or resid 24...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSGLYGLY(chain A and (resid 10 through 22 or resid 24...AA10 - 221 - 13
12PROPROILEILE(chain A and (resid 10 through 22 or resid 24...AA24 - 2615 - 17
13VALVALVALVAL(chain A and (resid 10 through 22 or resid 24...AA28 - 6519 - 56
14GLYGLYTYRTYR(chain A and (resid 10 through 22 or resid 24...AA67 - 6958 - 60
15VALVALVALVAL(chain A and (resid 10 through 22 or resid 24...AA7162
16ILEILEILEILE(chain A and (resid 10 through 22 or resid 24...AA73 - 8464 - 75
17PROPROTYRTYR(chain A and (resid 10 through 22 or resid 24...AA86 - 11477 - 105
18TYRTYRTHRTHR(chain A and (resid 10 through 22 or resid 24...AA116 - 118107 - 109
19ALAALAASNASN(chain A and (resid 10 through 22 or resid 24...AA120 - 124111 - 115
21CYSCYSGLYGLY(chain B and (resid 10 through 22 or resid 24...BB10 - 221 - 13
22PROPROILEILE(chain B and (resid 10 through 22 or resid 24...BB24 - 2615 - 17
23VALVALVALVAL(chain B and (resid 10 through 22 or resid 24...BB28 - 6519 - 56
24GLYGLYTYRTYR(chain B and (resid 10 through 22 or resid 24...BB67 - 6958 - 60
25VALVALVALVAL(chain B and (resid 10 through 22 or resid 24...BB7162
26ILEILEILEILE(chain B and (resid 10 through 22 or resid 24...BB73 - 8464 - 75
27PROPROTYRTYR(chain B and (resid 10 through 22 or resid 24...BB86 - 11477 - 105
28TYRTYRTHRTHR(chain B and (resid 10 through 22 or resid 24...BB116 - 118107 - 109
29ALAALAASNASN(chain B and (resid 10 through 22 or resid 24...BB120 - 124111 - 115

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12606.103 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 BL21 (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-BM8 / 4-(1,3-benzothiazol-2-yl)-2-methyl-aniline


Mass: 240.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.34 Å3/Da / Density % sol: 47.35 % / Mosaicity: 0.05 °
Crystal growTemperature: 293 K / Method: evaporation
Details: acetate buffer 0.2 M pH 4.8-5.4, ammonium sulfate 1.8-2.2 M, 7% glycerol
PH range: 4.8-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 7, 2016
Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.31→42.75 Å / Num. obs: 56993 / % possible obs: 99.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.014 / Rrim(I) all: 0.03 / Net I/σ(I): 21.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.31-1.364.30.73855630.680.3910.8499.6
5.07-42.753.80.01810640.9990.010.02196.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.25data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1y1d

1y1d


Resolution: 1.38→42.75 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.13
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 2498 5.12 %0.05
Rwork0.1602 ---
obs0.162 48775 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.44 Å2 / Biso mean: 26.3494 Å2 / Biso min: 12.64 Å2
Refinement stepCycle: final / Resolution: 1.38→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 34 106 1916
Biso mean--55.37 38.96 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061901
X-RAY DIFFRACTIONf_angle_d0.9122604
X-RAY DIFFRACTIONf_chiral_restr0.091292
X-RAY DIFFRACTIONf_plane_restr0.007329
X-RAY DIFFRACTIONf_dihedral_angle_d8.5681050
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A900X-RAY DIFFRACTION10.187TORSIONAL
12B900X-RAY DIFFRACTION10.187TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.40650.2641370.2152529266699
1.4065-1.43530.24941300.19982536266699
1.4353-1.46650.22941190.18232548266799
1.4665-1.50060.23081280.16825662694100
1.5006-1.53810.21331450.15542565271099
1.5381-1.57970.1881330.14292566269999
1.5797-1.62620.18741480.13252505265399
1.6262-1.67870.21431270.1332576270399
1.6787-1.73870.18531390.13822560269999
1.7387-1.80830.16911370.13612534267199
1.8083-1.89060.18051420.13172566270899
1.8906-1.99030.16831250.12892586271199
1.9903-2.1150.16821340.13762555268999
2.115-2.27820.17511680.144525862754100
2.2782-2.50750.20991270.15772619274699
2.5075-2.87030.21321650.17912580274599
2.8703-3.61590.1811380.16362609274798
3.6159-42.7750.20181560.1782691284796

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