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- PDB-9h7a: Human Transthyretin in Complex with 3,5-Dichlorobenzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 9h7a
TitleHuman Transthyretin in Complex with 3,5-Dichlorobenzenesulfonamide
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidosis / Retinol / Thyroxine / RBP
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
3,5-dichlorobenzene-1-sulfonamide / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsChen, W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
University of College LondonBXTX United Kingdom
Other privateHN9A
Citation
Journal: Plos One / Year: 2025
Title: Fragment-based drug discovery for transthyretin kinetic stabilisers using a novel capillary zone electrophoresis method.
Authors: Chen, W.
#1: Journal: Biorxiv / Year: 2025
Title: Fragment-Based Drug Discovery for Transthyretin Kinetic Stabilisers Using a Novel Capillary Zone Electrophoresis Method
Authors: Chen, W.
History
DepositionOct 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author

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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)27,7813
Polymers27,5552
Non-polymers2261
Water59433
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5626
Polymers55,1094
Non-polymers4522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6250 Å2
ΔGint-43 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.540, 43.450, 64.630
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
11B-201-

6OT

21B-201-

6OT

31B-201-

6OT

41B-311-

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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Human Plasma / Gene: TTR, PALB / Production host: Homo sapiens (human) / Tissue (production host): Human Plasma / References: UniProt: P02766
#2: Chemical ChemComp-6OT / 3,5-dichlorobenzene-1-sulfonamide


Mass: 226.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5Cl2NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 200 mM CaCl2, 28% v/v PEG400, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.76→64.63 Å / Num. obs: 24574 / % possible obs: 99.99 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.047 / Net I/σ(I): 18.9
Reflection shellResolution: 1.76→1.807 Å / Rmerge(I) obs: 1.339 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1551 / Rpim(I) all: 0.554

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→51.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.284 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22649 1255 5.1 %RANDOM
Rwork0.19456 ---
obs0.19622 23284 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.329 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.76→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 12 33 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021776
X-RAY DIFFRACTIONr_bond_other_d0.0030.021132
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9412439
X-RAY DIFFRACTIONr_angle_other_deg0.93232774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.535238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33222.54259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17315252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.366156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
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: 1.761→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 98 -
Rwork0.223 1551 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32440.2904-0.13970.8438-0.24650.9544-0.0241-0.07580.01520.0418-0.03280.1224-0.0441-0.03340.05690.0395-0.00820.02040.0156-0.01240.0378-13.09122.508-6.556
21.5227-0.05580.30781.3013-0.67161.1577-0.08490.2113-0.0595-0.1210.05160.2191-0.0283-0.11010.03340.0739-0.0211-0.03590.0743-0.02150.0705-12.84619.22-25.551
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 124
2X-RAY DIFFRACTION2B11 - 123

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