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- PDB-8hej: Crystal structure of Transthyretin in complex with a covalent inh... -

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Basic information

Entry
Database: PDB / ID: 8hej
TitleCrystal structure of Transthyretin in complex with a covalent inhibitor trans-styrylpyrazole
ComponentsTransthyretin
KeywordsHORMONE / Inhibitor
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
2,4,6-trifluorobenzaldehyde / Chem-XHF / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKim, H. / Choi, S. / Lee, C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M3A9G8022417 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of Transthyretin in complex with a covalent inhibitor trans-styrylpyrazole
Authors: Lee, S. / Choi, S.
History
DepositionNov 8, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)26,0706
Polymers25,0062
Non-polymers1,0644
Water2,684149
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,14012
Polymers50,0124
Non-polymers2,1298
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)84.945, 42.685, 64.272
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-201-

XHF

21A-201-

XHF

31A-201-

XHF

41B-201-

XHF

51B-201-

XHF

61B-201-

XHF

71B-357-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12502.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-XHF / 2,6-dibromo-4-[(E)-2-(3,5-dimethyl-1H-pyrazol-4-yl)ethenyl]phenol


Mass: 372.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12Br2N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XHB / 2,4,6-trifluorobenzaldehyde


Mass: 160.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H3F3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: Sodium Citrate pH5.5, Glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 88572 / % possible obs: 99.9 % / Redundancy: 14.2 % / CC1/2: 0.999 / Net I/σ(I): 48.7
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 88572 / CC1/2: 0.868

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HJ0

3hj0


Resolution: 1.54→30.107 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1515 4.3 %
Rwork0.1858 --
obs0.1875 35271 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→30.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 58 149 1973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111905
X-RAY DIFFRACTIONf_angle_d1.1622602
X-RAY DIFFRACTIONf_dihedral_angle_d6.2022248
X-RAY DIFFRACTIONf_chiral_restr0.082291
X-RAY DIFFRACTIONf_plane_restr0.009330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.58970.25611350.23373026X-RAY DIFFRACTION100
1.5897-1.64650.26791360.22933031X-RAY DIFFRACTION100
1.6465-1.71240.26261370.23233030X-RAY DIFFRACTION100
1.7124-1.79040.271360.23313021X-RAY DIFFRACTION100
1.7904-1.88480.23441350.21483038X-RAY DIFFRACTION100
1.8848-2.00280.22711370.18093032X-RAY DIFFRACTION100
2.0028-2.15740.18761370.17583070X-RAY DIFFRACTION100
2.1574-2.37440.21851390.17873076X-RAY DIFFRACTION100
2.3744-2.71780.2091380.19153080X-RAY DIFFRACTION100
2.7178-3.42340.21041400.17733127X-RAY DIFFRACTION100
3.4234-30.1070.23091450.17163225X-RAY DIFFRACTION98
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)
14.70864.3773-6.23894.0594-5.8098.1990.2184-0.4299-0.28050.5997-0.4657-0.22-0.19320.40330.2720.153-0.0058-0.00740.17170.03070.147-7.4291.437-2.67
25.0759-0.2307-6.02380.35470.25557.1288-0.0808-0.11260.51830.12540.06320.152-0.0935-0.0674-0.17290.1424-0.0068-0.01350.1484-0.03320.2052-4.65812.047-5.498
33.50984.87740.08997.7963-1.1272.9442-0.0830.29910.0235-0.51340.09750.47950.2548-0.399-0.11490.16610.0001-0.00970.24-0.04340.2949-24.485-4.929-7.901
45.58891.11732.14985.5883.59197.7580.062-0.30910.2648-0.0391-0.43910.57770.1204-0.46880.42660.1330.03230.03770.15230.01370.2011-22.596-0.704-3.933
53.74614.8666-3.38517.1477-4.76773.40280.237-0.660.05020.3901-0.36630.06-0.19790.32470.1750.1785-0.01660.01040.2441-0.01880.1469-9.3464.9492.474
68.33516.57895.36415.28264.45294.15170.0345-0.226-0.28140.3855-0.07750.17180.54370.0384-0.02320.2113-0.00180.06440.17070.02090.2297-19.628-10.6363.687
72.93543.1438-0.44456.7512-2.39682.7075-0.16370.0090.3676-0.05750.14990.6337-0.2329-0.20160.00430.17330.0486-0.00770.1575-0.010.1672-15.0185.356-10.023
83.72130.176-0.51587.53275.37616.7064-0.19660.29660.2230.5241-0.0045-0.7509-1.0817-0.08890.11150.3119-0.0172-0.1010.12510.07140.2039-12.28312.105-16.842
98.14712.8483-7.12793.4202-5.33579.8030.0668-0.027-0.05460.0523-0.04260.0046-0.3072-0.1143-0.2130.1484-0.0053-0.0110.14670.0020.1213-15.153-6.348-10.418
103.12682.1039-1.62357.5065-4.8865.70540.0142-0.1211-0.22690.1191-0.1338-0.04570.07310.13880.12750.09920.01050.00790.1357-0.01250.1055-7.859-5.033-7.16
113.3769-0.57522.57855.7578-6.4438.28380.16720.66440.1102-0.4649-0.32190.04840.02710.33210.23410.2098-0.0351-0.02720.1963-0.01940.1299-7.094-2.572-29.476
126.9550.66986.43260.29821.29088.70910.07270.3229-0.4079-0.21790.0704-0.00860.02060.1105-0.35570.1786-0.01310.00980.2093-0.04970.1959-2.267-12.43-26.5
136.0712-5.1235-2.86854.3142.60288.1284-0.17140.152-0.57220.4518-0.21531.1851-0.127-1.08770.27530.23280.00160.00850.3239-0.01850.3772-24.5850.602-24.087
143.1699-0.6718-4.48346.19284.65488.65-0.1190.1523-0.40410.286-0.34560.9396-0.1924-0.31940.61230.2378-0.0059-0.03260.1932-0.01120.2593-22.168-3.21-28.237
153.4209-2.772.92373.4465-3.59654.00970.16491.1120.1293-0.543-0.5187-0.0585-0.16210.5030.4120.29820.0038-0.02620.35850.00140.1816-8.329-6.287-34.68
164.8083-5.0367-5.77435.24096.0066.96060.13330.0797-0.0125-0.3447-0.1761-0.1667-0.5639-0.07610.1880.32430.0212-0.10790.28810.00220.3374-20.4147.527-35.849
177.105-5.48382.64734.8857-3.47574.12040.19330.0583-0.6012-0.1474-0.19421.0542-0.174-0.1315-0.05060.1727-0.0151-0.03150.2177-0.00250.2154-17.938-1.21-23.586
189.2234-1.8668-2.88836.71014.2733.1158-0.16360.2153-0.7405-0.03830.08710.24110.4236-0.0870.1870.2063-0.017-0.00050.14790.01830.2147-8.82-16.103-20.655
195.8945-0.3695-3.44255.13923.6284.30150.1041-0.0886-0.3131-0.2491-0.14520.15230.3211-0.12440.08760.19-0.0009-0.02620.18330.05320.2149-10.489-13.153-14.549
205.1645-1.283.85794.7963-3.41674.3002-0.0257-0.1504-0.0840.48090.17320.3204-0.21360.0736-0.27860.20160.01810.00580.17220.02420.1546-15.8193.551-21.706
210.2671-0.43160.15621.7780.89083.9603-0.0080.19990.96960.2077-1.4271-1.7343-0.75141.72691.45630.74270.1736-0.01510.76310.33110.862-13.62115.543-31.864
224.4379-2.15292.02512.0686-1.75434.345-0.08910.40230.153-0.0356-0.0590.009-0.3573-0.03220.14160.1814-0.026-0.02890.2147-0.00430.1449-7.1340.841-26.563
233.7077-0.40560.55987.5329-4.92257.553-0.08510.29650.1824-0.14760.0059-0.1181-0.1363-0.10830.08410.1477-0.03-0.00010.1815-0.02480.1196-5.6090.497-21.341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:18 )A11 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:28 )A19 - 28
3X-RAY DIFFRACTION3( CHAIN A AND RESID 29:40 )A29 - 40
4X-RAY DIFFRACTION4( CHAIN A AND RESID 41:48 )A41 - 48
5X-RAY DIFFRACTION5( CHAIN A AND RESID 49:58 )A49 - 58
6X-RAY DIFFRACTION6( CHAIN A AND RESID 59:66 )A59 - 66
7X-RAY DIFFRACTION7( CHAIN A AND RESID 67:81 )A67 - 81
8X-RAY DIFFRACTION8( CHAIN A AND RESID 82:90 )A82 - 90
9X-RAY DIFFRACTION9( CHAIN A AND RESID 91:97 )A91 - 97
10X-RAY DIFFRACTION10( CHAIN A AND RESID 98:124 )A98 - 124
11X-RAY DIFFRACTION11( CHAIN B AND RESID 11:18 )B11 - 18
12X-RAY DIFFRACTION12( CHAIN B AND RESID 19:28 )B19 - 28
13X-RAY DIFFRACTION13( CHAIN B AND RESID 29:40 )B29 - 40
14X-RAY DIFFRACTION14( CHAIN B AND RESID 41:48 )B41 - 48
15X-RAY DIFFRACTION15( CHAIN B AND RESID 49:58 )B49 - 58
16X-RAY DIFFRACTION16( CHAIN B AND RESID 59:66 )B59 - 66
17X-RAY DIFFRACTION17( CHAIN B AND RESID 67:74 )B67 - 74
18X-RAY DIFFRACTION18( CHAIN B AND RESID 75:82 )B75 - 82
19X-RAY DIFFRACTION19( CHAIN B AND RESID 83:90 )B83 - 90
20X-RAY DIFFRACTION20( CHAIN B AND RESID 91:97 )B91 - 97
21X-RAY DIFFRACTION21( CHAIN B AND RESID 98:103 )B98 - 103
22X-RAY DIFFRACTION22( CHAIN B AND RESID 104:112 )B104 - 112
23X-RAY DIFFRACTION23( CHAIN B AND RESID 113:124 )B113 - 124

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