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- PDB-9h7c: Human Transthyretin in Complex with 4-(1H-imidazol-1-yl)phenol -

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Basic information

Entry
Database: PDB / ID: 9h7c
TitleHuman Transthyretin in Complex with 4-(1H-imidazol-1-yl)phenol
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) / 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, 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
4-(1H-IMIDAZOL-1-YL)PHENOL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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)27,9556
Polymers27,5552
Non-polymers4014
Water1,74797
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,91012
Polymers55,1094
Non-polymers8018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8200 Å2
ΔGint-77 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.034, 85.040, 63.639
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-

MSR

21A-202-

MSR

31B-301-

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: 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-MSR / 4-(1H-IMIDAZOL-1-YL)PHENOL


Mass: 160.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
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: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 59970 / % possible obs: 98.5 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.026 / Net I/σ(I): 13.3
Reflection shellResolution: 1.27→1.303 Å / Rmerge(I) obs: 0.609 / Num. unique obs: 3748 / Rpim(I) all: 0.338 / % possible all: 89.36

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→35.35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.533 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20869 3038 5.1 %RANDOM
Rwork0.16572 ---
obs0.16778 56888 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.708 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.27→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 26 97 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191765
X-RAY DIFFRACTIONr_bond_other_d0.0010.021575
X-RAY DIFFRACTIONr_angle_refined_deg2.1561.9522428
X-RAY DIFFRACTIONr_angle_other_deg0.94233617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2655233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00723.50957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48815228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.6152
X-RAY DIFFRACTIONr_chiral_restr0.1550.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
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_it2.9141.548916
X-RAY DIFFRACTIONr_mcbond_other2.9141.549917
X-RAY DIFFRACTIONr_mcangle_it3.3322.331144
X-RAY DIFFRACTIONr_mcangle_other3.3372.3291143
X-RAY DIFFRACTIONr_scbond_it3.5121.826849
X-RAY DIFFRACTIONr_scbond_other3.511.827850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0752.6391281
X-RAY DIFFRACTIONr_long_range_B_refined4.23213.7971929
X-RAY DIFFRACTIONr_long_range_B_other4.23213.8021930
X-RAY DIFFRACTIONr_rigid_bond_restr7.84933339
X-RAY DIFFRACTIONr_sphericity_free16.291523
X-RAY DIFFRACTIONr_sphericity_bonded9.58653362
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 200 -
Rwork0.236 3748 -
obs--89.36 %

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