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- PDB-5a6i: V122I Transthyretin structure in complex with Tolcalpone -

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Basic information

Entry
Database: PDB / ID: 5a6i
TitleV122I Transthyretin structure in complex with Tolcalpone
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / TRANSPROT PROTEIN / TRANSTHYRETIN / AMYLOID
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
Tolcapone / Transthyretin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsReverter, D. / Gallego, P. / Santana, R. / Ventura, S.
CitationJournal: Nat.Commun. / Year: 2016
Title: Repositioning Tolcapone as a Potent Inhibitor of Transthyretin Amyloidogenesis and its Associated Cellular Toxicity
Authors: Reverter, D. / Gallego, P. / Santana, R. / Ventura, S.
History
DepositionJun 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1962
Polymers13,9231
Non-polymers2731
Water41423
1
A: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7838
Polymers55,6904
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation2_565-x,-y+1,z1
Buried area6180 Å2
ΔGint-43 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.484, 62.547, 84.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1124-

TCW

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Components

#1: Protein TRANSTHYRETIN / ATTR / PREALBUMIN / TBPA


Mass: 13922.583 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-147 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-TCW / Tolcapone / (3,4-dihydroxy-5-nitrophenyl)(4-methylphenyl)methanone


Mass: 273.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11NO5 / Comment: medication, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.12 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 38169 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.5
Reflection shellResolution: 1.86→1.87 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→50.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.079 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27084 493 5.1 %RANDOM
Rwork0.19702 ---
obs0.20066 9250 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.446 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2--2.03 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.86→50.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 20 23 925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9521295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81323.51437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25115145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.868154
X-RAY DIFFRACTIONr_chiral_restr0.1230.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021729
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_restr6.923946
X-RAY DIFFRACTIONr_sphericity_free24.39759
X-RAY DIFFRACTIONr_sphericity_bonded13.8315933
LS refinement shellResolution: 1.862→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 33 -
Rwork0.245 616 -
obs--99.54 %
Refinement TLS params.Method: refined / Origin x: 1.2489 Å / Origin y: 21.5076 Å / Origin z: 97.6651 Å
111213212223313233
T0.0401 Å2-0.0073 Å2-0.0321 Å2-0.049 Å20.0237 Å2--0.0845 Å2
L4.6481 °21.0695 °2-3.249 °2-2.6346 °2-1.9345 °2--7.0681 °2
S0.1683 Å °-0.3851 Å °-0.0993 Å °0.1704 Å °-0.0273 Å °0.0462 Å °-0.1197 Å °0.3751 Å °-0.141 Å °

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