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- PDB-9h7e: Human Transthyretin in Complex with 4-pyridin-3-ylbenzoic acid -

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Basic information

Entry
Database: PDB / ID: 9h7e
TitleHuman Transthyretin in Complex with 4-pyridin-3-ylbenzoic acid
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
4-(pyridin-3-yl)benzoic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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)27,9935
Polymers27,5552
Non-polymers4383
Water84747
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,98610
Polymers55,1094
Non-polymers8776
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)84.123, 41.221, 63.481
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-

PQM

21B-201-

PQM

31B-201-

PQM

41B-201-

PQM

51B-201-

PQM

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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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PQM / 4-(pyridin-3-yl)benzoic acid


Mass: 199.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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 Å3/Da / Density % sol: 38.41 %
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: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.43→41.22 Å / Num. obs: 41021 / % possible obs: 99.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 1.432→1.469 Å / Rmerge(I) obs: 0.532 / Num. unique obs: 2618 / Rpim(I) all: 0.379 / % possible all: 97.98

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→37.02 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.291 --RANDOM
Rwork0.23656 ---
obs0.23925 38932 98.95 %-
Refinement stepCycle: LAST / Resolution: 1.43→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 31 47 1531

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