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- PDB-9h7j: Human Transthyretin in Complex with 5-methyl-4-phenyl-1H-pyrazol-... -

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Basic information

Entry
Database: PDB / ID: 9h7j
TitleHuman Transthyretin in Complex with 5-methyl-4-phenyl-1H-pyrazol-3-amine
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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)27,9816
Polymers27,5552
Non-polymers4274
Water75742
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,96312
Polymers55,1094
Non-polymers8538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)84.480, 42.020, 63.490
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-202-

A1ISY

21A-202-

A1ISY

31A-202-

A1ISY

41B-201-

A1ISY

51B-201-

A1ISY

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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: Blood / Gene: TTR, PALB / Production host: Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1ISY / 5-methyl-4-phenyl-1H-pyrazol-3-amine


Mass: 173.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 294.15 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: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→42.02 Å / Num. obs: 56419 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.017 / Net I/σ(I): 23.4
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 4105 / Rpim(I) all: 0.247

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→31.75 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.091 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26024 2855 5.1 %RANDOM
Rwork0.22528 ---
obs0.22705 53512 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å20 Å2
2--0.75 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.3→31.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 28 42 1611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0191626
X-RAY DIFFRACTIONr_bond_other_d0.0020.021416
X-RAY DIFFRACTIONr_angle_refined_deg3.0281.9542239
X-RAY DIFFRACTIONr_angle_other_deg1.14133232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6185218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.18723.12548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31315188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.604151
X-RAY DIFFRACTIONr_chiral_restr0.1830.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211859
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02374
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_it3.081.734870
X-RAY DIFFRACTIONr_mcbond_other3.0821.732869
X-RAY DIFFRACTIONr_mcangle_it3.4062.6141081
X-RAY DIFFRACTIONr_mcangle_other3.4052.6161082
X-RAY DIFFRACTIONr_scbond_it3.3661.965756
X-RAY DIFFRACTIONr_scbond_other3.3641.965757
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7772.8661156
X-RAY DIFFRACTIONr_long_range_B_refined3.93315.1851706
X-RAY DIFFRACTIONr_long_range_B_other3.93115.1851707
X-RAY DIFFRACTIONr_rigid_bond_restr8.97333040
X-RAY DIFFRACTIONr_sphericity_free19.036511
X-RAY DIFFRACTIONr_sphericity_bonded15.0653026
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 209 -
Rwork0.261 3888 -
obs--99.88 %

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